The amazing hybrid of mod design document and a fanfic.

The “In-Game” form of the fanfic:

Some knowledge of the base game’s story is needed for this, as many events happen around the same time, and stages are visited in a timeframe of ‘before’ or ‘after’ main heroes.

Some extra notes:

Intro cutscene :

(Both happen before their FP2 equivalents)

– Three years ago –
A small space station silently floats above Avalice, with it’s hull covered in antennas and a name:
ARS Wayfinder written on it’s surface - a barcode and several worn out flags surround the name, but are too worn out to identify.
A shadow is cast upon it, as the camera zooms out showing Final Dreadnought eclipsing the sun. A volley of shots gets fired onto the station heavily damaging it as both vessels soon fall onto the planet.

– Current Day –

Back in the present, Kubo is napping aboard a nighttime train headed for Shang Tu - the train itself named Shang Mu express, in case the colour scheme and pictures of Mayor Zao’s hat did not make it quite obvious already to who funded this train line.
Train sudden breaks, waking up Kubo and other passengers. He makes a dissapointed sigh - not only his sleep was cut short, but the train is now guaranteed to be late - and all Zao Railways will offer in such case is a 5% off coupon for the next ticket ([over certain price ([on qualifying routes ([only on specific hours ([only on Mondays ([non-refundable))))]]]]

A short announcement is played:
Dear passengers, we seem to have encountered an unexpected delay on our route due to-
** Proto Pincer rolls into the train, shaking the whole cart **
-this THING outside. We greatly apologise for the inconvenience, and will inform you as soon as we get updates on the situation.

Sighs and sound of annoyance from the passengers follow, as the train very slowly moves to a nearby station.

Hub 1: Dragon Road Train station

(Events before intro cutscene for the main group)

A small hub, equivalent to the base game’s Singing Water Temple
Contains shop with slightly expanded inventory - unlike the base game, you get to choose your starter stones here instead of a difficulty menu. ‘Easy mode’ stones are available for free.

In the area you get to visit quickly set up shop, talk to several annoyed or just tired NPC.
Once going enough to the left or right, another announcement is played, this time informing that the train will likely have to stay here for a day.
When the announcement is finished, Kubo decides that he will likely get to the city faster going on foot than waiting for the train to move again. You can now leave the hub and proceed to Dragon Valley.

Once progressed further into the story revisiting the area shows that the train is gone, and only few NPC stick around.

Stage 1: Dragon Valley

(Stage visited before the main characters)
Same stage as in base game (it’s going to be a common thing), once Proto Pincer gets defeated at the end of the stage, it escapes instead of being destroyed - it will later go on to fight Lilac and the team.

World Map cutscene 1:

A short exchange occurs between Kubo, and a contact from his current contractor Three Kingdom News.
Arriving just in time for his job, the task is to distract the robotic invaders (and potentially deal with their source), so the TV crew can make a report on the attack in relative safety.

Stage 2: Shenlin Park

(Stage happens at roughly the same time as the main characters)
Same stage, however the radio chatter is replaced with Maria Notte’s ongoing report on the situation.

Most TKN contract levels also include small ‘REC’ symbol on the screen, as parts of them end in the news broadcast.

Post Stage Cutscene:

After defeating Trigger Joy, Maria lands next to Kubo congratulating him on the work done. While he cannot really tell if it’s genuine thanks, or just part of the station’s policy, he smiles back regardless, and after a short friendly chatter they part ways.

World Map cutscene 2:

Game’s ‘choose next story’ menu is available, letting you choose from 2 different contracts.

Hub 2: Shang Tu Palace Daytime

Same-ish hub as the base game, however since civilians are not allowed inside the palace few NPC merchants are moved around to account for that.
You can still spar in the Dojo if you wish, Gong mentions that Lilac and the rest always welcome new partners to spar with. Askal however refuses to fight you.

(Story occurs at the similar time as the main heroes, but slightly before them agreeing to work for the Magister)
Area unlocks regardless of the contract chosen, however cutscenes only play out on Contract 2.

You visit the hub for similar reasons as the main crew - to get the job briefing from General Gong.
Since you cannot enter the palace proper, the briefing room is shown only in the cutscene itself before being sent back outside.

Shuigang Arc Intro (Contract 1):

Stage 3: Tiger Falls

No changes from base game

Hub 3: Shuigang

No layout changes

(After main heroes took off to RD, but before they reported seeing Brevon’s forces there)

King Dail explains you the details of the job - same task as main heroes, however Kubo gets sent off to another part of the FD crashsite, due to reports of unusual activity in that region.

Did you know? Maria actually appears and has unique dialogue in this hub in base game, but only if you do Shuigang chapter first.
In the mod she’s always there, regardless of when this chapter is being done.

World Map Cutscene 3:

After leaving Shuigang hub, Kubo gets a call from his main employer - archaeologist Millie, who currently resides in Parusa investigating remnants of water dragon culture. After finding out Kubo is currently in Shuigang, she explains thats exactly what she needed to hear, and asks him to take a detour on his task - she needs him to locate another smaller crash site of a ship that fell alongside Final Dreadnought. The site is not far away from Robot Graveyard, and she will be extremely gratefull if Kubo were to obtain any information on the origin of the alien ship.

Stage 4: Robot Graveyard

(Same time as main heroes)
Similar layout to normal version of the stage, however with much lower presence of Brevon’s forces - they seem to have moved closer to the center due to a disturbance there (aka team Lilac appearing there).
End of level arena is replaced with fight against Serpentine. Serp was slowly getting desperate in his search for working Syntax drone, and both of you meet eachother on the way to the crashed ship - Serpentine hoped he could salvage it’s communication array to call for Brevon’s fleet (which makes it very obvious Brevon is not here, nor he cares about what happened to Serpentine). To Serpentine’s anger Kubo has no idea who he is.

You do not fight Wolf Armor, but only the Phase 1 Serpentine with extended health and extra attacks. It would not make much sense for him to carry that thing with him everywhere afterall.

Following the fight Serpentine darts off defeated, saying something about how his retreat is merely a ‘mercy of lord Brevon’.

A cutscene plays out where Kubo locates the shipwreck and Millie instructs him to hack into the ship and retreive it’s datacores. [Hacking minigame maybe?]
After opening the core compartment, only one core is present.

A ‘Time Capsule Got’ cutscene plays, announcing you have obtained Data Core #2

Along with the core, Millie asks Kubo to collect a gold disc with pictures drawn on it - something for museum in Shang Tu to show off.

It’s the same disc Voyager probes carried irl. containing information on Terra on one side, and vinyl audio recording on the other.

Ship’s telemetry states that remaining datacores were ejected before the crash according to it’s emergency policies. Location of few nearby cores gets revealed (nearby mountain area, Shuigang, and few blips for Shang Mu and Shang Tu regions), with total count of cores standing at 12.
Millie deduces that it’s likely that Serpentine holds one of them due to it’s position, sending Kubo off to retreive it.

Stage 5: Shade Armory

(Slightly after main heroes - At this time they already are after Serpentine )
Stage is roughly the same, however you obtain Data Core #3 midway trough it [unskippable >:3].
At the end you fight Syntax Spider like the main group. Kubo notes he once saw a similar drone at a museum.

Shuigang Arc ending:

(After the main heroes)
Kubo returns to Shuigang where Dail mentions that while another team has already found the source of the disturbance, he is a man of his word and pays him for the job done.
He also apologizes for putting Kubo in harm’s way as he did not anticipate Brevon’s troops to be still active in the area.

Sigwada Arc Intro (Contract 2):

(Before the main heroes)
General Gong’s briefing suggested to take a shortcut trough Avian Museum - on arrival the place is already overrun by hostile robots, forcing Kubo to fight trough them.

Stage 6: Avian Museum

Same stage with no major changes

(Before the main heroes)
After the boss fight, AAA is greatly confused who is this guy who just broke one of their robots, ending the exchange with:
“*THAT TRAP WASNT EVEN MEANT FOR YOU AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAUGH - faints”
Kubo just stares at the show with ‘who’s that… sassy lost child’ face.

World Map Cutscene 4:

Just like he warns main group, Gong calls you with information that Sigwada is lying siege on the airship docks and Shang Tu defence fleet is failing do stop it. He says that since Kubo’s ship is not blown up yet, he’s one of the few people who can still oppose it.
At this point Kubo is already slightly amused by the irony of his ship being possibly wrecked a second time by an enemy invasion fleet.

Stage 7: Airship Sigwada

Completely custom SHMUP stage.

(Same time as main group)
Intro cutscene has Kubo getting to his ship as Sigwada lays siege to area around it, and taking off to take it head on.

Shmup stage is similar to base game’s Bakunawa Chase, but since it is happening much earlier in the game with slightly lowered difficulty by the virtue of you having extra firepower. Kubo’s ship comes equipped with plasma guns (comparable to firework guns of Zao’s ship), homing missiles, and ability to charge ahead damaging enemies in the way of the dash. Finally, it also has a front mounted laser, similar to one used in FP1’s shmup section, which needs half a second of initial charge to fire and which consumes entirety of the charge meter.

Boss of the stage is Sigwada itself, equipped with its arrow missile front cannon and several classic missile and projectile launchers. Due to it’s sheer scale you only see the front of the ship outside of cutscene zoomouts.
Sigwada pulls out of the fight when enough damage is dealt to it’s hull and laser cannon, and Corazon

At the same time, the main heroes board the ship due to distraction the fight caused, leading to events of the base game’s stage.

Sigwada Arc Ending

(Events happen after main heroes finished their Sigwada arc)
After returning to Shang Tu you get debriefed by Gong, who mentions that Kubo’s ship seems to be one of the very few which survived Sigwada’s attack.
As a reward for the help, Gong gives you one of the artifacts from the museum that the attackers tried to steal

A ‘Time Capsule Got’ cutscene plays, announcing you have obtained Data Core #5, just to get interrupted in the middle by Gong being all like ‘does everyone have to dance when they pick up an item’

Battlesphere Arc Intro:

After completing both contracts, the final 3rd contract becomes available.
Sent off by Three Kingdom News it includes travelling to Shang Mu, and securing an interview with Captain Kalaw - the current Battlesphere champion refuses to perform an interview unless met by strong enough challenger.
Initially Kubo is not interested in the job, mainly due to the need of travel all the way back to Shang Mu, however he agrees in the end, possibly because of a certain bat being sent there too.

Hub 4: BattleSphere Lobby

Pheonix Highway and ZaoLand are skipped here, as Kubo travels to Shang Mu by his airship. World map paths are changed accordingly.

Arriving before the main heroes, Kubo meets with Maria in the lobby. She explains that Kalaw’s refusal to take interviews seems very suspicious to her, as he is not known to ever shy from showing himself on air. The reporter senses are tingling, and she wants to find out why Kalaw acts like this all of the sudden.

“Stage” 8: Battlesphere gauntlet

(Events happen before the ones from the main game)

Similar experience to base game, however:

After beating the initial challenges, Kalaw makes his fancy appearance, followed by equally fancy exchange - Kubo knows well enough how the champion talks, and replies in the same vein (similar to how Lilac did, but in a bit more taunting way).

Kubo likely spends entire week worth of social courage to speak like that in front of an audience.

As in the base game, Kalaw offers one final challenge - the wheel of fate lands on Home Run.
The Home Run Challenge is only a bit similar to the main game’s an in this VS. iteration you instead clear a longer course while breaking as many targets as possible (and not just launch on a ball once). Kalaw runs the course as well, and while it is easy-ish to beat his “score” (preset value), he can break the targets on his way making it harder to get the needed score.

After winning the challenge, Kalaw goes on how grand the show was (but implying he let you win, which is not the truth) and agrees to resume the interviews for TKN after he deals with his ‘errands’.
Award ceremony starts and mayor Zao comes up the lift with the box of wonders, which after epic opening animation reveals a ‘cheap trinket he found’ - Data core #7.
Zao then ponders what to award the next contenders as he seems to have ran out of cheap items to give away.

Battlesphere Arc ending - Opera Arc start

(Events happen before the ones from the main game)

After returning to lobby Kubo returns to Maria to relay the good news.
When that is over Kubo wonders if he should try his luck and ask her out somewhere. A menu options appear:

No matter what the player chooses, the next dialogue gets interrupted by city-wide alert about Mayor Zao’s abduction and hostile presence at the Globe Opera. While Kubo would prefer to stay put, Maria flies off to the scene of the new and exciting report, and Kubo decides to follow her just to make sure nothing bad happens.

Arriving at the scene Maria somehow managed to already interview several guards blocking the way and the bystanders.
Two of the guards are preparing to storm the Opera in attempt to rescue their employer - when they recognise Kubo as a winner of today’s battlesphere course they offer him to join in - while reluctant, he gets convinced by Maria to take the offer and bring a portable camera drone along with him to gather footage from the inside. He really can’t say no to ‘sad bat puppy eyes’.

Stages 9-11: Globe Opera

Acts 1 and 2 are identical to the base game

(Events happen before the ones from the main game)

Arriving at the center of the opera, the main Auditorium Kubo and the guards encounter AAA and Corazon (Kalaw is not there). Aaa screams that they have met that cat before and they wrecked their stuff, and that they managed to trip another trap not meant for them. Beast 3 gets sent off and a boss fight starts (two guards jump off to fight Aaa and Cory directly).
Once the fight is over, it’s shown that the guards managed corner Cory and Aaa (who is currently screaming about lacking a third pilot for their ‘Best Friend’) when Merga shows up.
>Not a hologram.
>She has not left the Opera yet.
>Oh no.
She congratulates the trio on their courage and orders them to drop their weapons. One of the guards starts shaking, but trapped Zao yells at him, which puts him back to battle stance. Merga simply states ‘So be it.’

The unwinnable Merga fight starts.
Zao’s guards have enough health to take 2-3 direct attacks from her. She attacks in the same way as in Palace Courtyard fight, however if you manage to beat her first ‘phase’ she pulls out the shadow knives from final boss fight.
Getting knocked down in this fight skips your stocks and proceeds straight to level end card.
Beating Merga is technically impossible, but if you beat her somehow the story proceeds the same way.

With both guards down Merga grabs Kubo by the tail and yeeets him at the wall. Instantly appearing by him to grab him by the neck, she states:
“Good news, Cat, for you are not the target today. I will let you live for now - do not stand in my way again”
before throwing him on the ground followed by the screen fading to black.

Opera Arc end - Parusa Arc Start

Palace Courtyard is skipped

(Unspecified time between Palace Courtyard in base game, and Carol leaving to Parusa)

Kubo wakes up aboard his airship, with Millie looking over him.
According to her the moment she realised he might get in trouble way over his grade, she took off from Parusa to help him. By the time she arrived Merga has already beaten him up, and threw him and Zao’s guards outside where Millie found them all knocked out. After checking for injuries she brought the guards to their friends at the entrance, and Kubo back to his ship, afterwards setting it on course for Parusa.

While knowing Millie quite well Kubo has not expected her to come all this way to rescue him - in fact he has never really met her in person as most of the time she would call, text, or videocall him instead.
Dialogue options let you ask about:

Hub 5: Ancient Dragon Research Outpost + Adventure Square

Custom Hub area connected to Adventure Square (implied close enough to just walk there and to be connected by a road)

The two arrive at the research outpost, landing the ship off to it’s side.
Place is populated by several buildings, some makeshift, others more complete, and populated by several researchers and a vendor - everyone’s beloved Chloe. Building feature several water dragon artifacts and statues, with bigger ruins of unspecified structures visible in the background - on the first sight just built out of stone however several broken off pieces show metal and wiring underneath.

Millie resides in one of the bigger buildings, containing her personal room, research workshop, and few storage areas.
Main feature of the workshop is a computer wired to piece of visibly more modern technology, similar to dragon technologies seen in other rooms and museums, yet somewhat different as if made by different makers altogether.
The device allows you to decipher Data Cores and see their contents - just like Time Capsules, however some entries are comprised of just text (as not all of them have video footage). A Core itself contains much more data, but it’s mainly telemetry and terabytes worth of geographical,botanical, and all the other kinds of, data.
Just like in base game, video Data Cores play a holographic recording of their contents - Kubo watches it by stepping back from the device while Millie rests against a back wall.

After a tour of the place (and watching one Data Core), Millie asks Kubo to collect the remaining ones while he is out doing his jobs.
When talking to her, depending on cores collected and story progress she will have different remarks on their contents and significance.

When Kubo is preparing to depart to Adventure Square, Millie asks him to deliver an item to the walking advertisement ““custodian”” of the local water dragon museum - she hands him an actual Time Capsule (playing the same jingle and all) to trade for a data core.
Once in the museum, Judie pulls out a Data Core #4 which was simply slammed into the console upstairs, before inserting the Time Capsule in it’s place which to her surprise fits perfectly.

Some Optional Content

In search for Data Cores, you can visit two previously skipped optional stages:

World Map cutscene 4:

Game’s second ‘choose next story’ menu is available, letting you choose from 2 different contracts.

Paradise Prime arc start:

Arriving back at Adventure Square Kubo reunites with Maria, first time after the events at the opera. She explains she was deathly worried when the drone footage cut off, thinking she sent Kubo off to his demise.
The chat is short, as the task is time sensitive, as nobody knows how long Kalaw will hang around the beacons he placed around the island - despite his words he does it to protect the region he seems inclined to leave as soon as possible.

Stage 12: Sky Bridge

(Events happen before main heroes get there)

Stage plays roughly the same, however the initial approach is done by Kubo’s airship instead of a small plane from the base game. You still fight off the same waves of enemies.

Mid-stage Millie calls you with information on the beacons, mentioning that they completely do not mach what Kalaw says about them, and that their power signature matches that of water dragon technology.

Boss fight with Kalaw plays out the same, however the dialogue plays out differently as Kalaw’s betrayal at Opera is not public knowledge yet, but at this point his motives are questionable at best. He does not directly admit to his actions, but in his pride he offers to let his actions be streamed live to prove his innocence (and we all know where that led).

Hub 6: Paradise Prime

Same hub as in the base game, Kubo’s ship is however docked by the airship docks, serving as another exit from the hub area.

Just as in the base game not much happens here. Place is quite pretty tho.
Millie calls Kubo with another request to obtain data cores from Lightning Tower - it’s magnetic field seems to have attracted a pair of them, both being relatively important.

Stage 13: Lightning Tower

(Events happen before the main game’s - early enough that Corazon is not around, with Sigwada currently circling near the volcano area).

Data Cores #1 and #8 are located in the stage, in chests - collecting them closes the circuit for the door opening mechanism making them not skippable.

Paradise Prime arc end

(Before Lilac (and the rest) reunite with Carol)
After returning from the floating island, Kubo and Maria finally have some free time after work.
You are once again given an option to try asking her out on a date - and this time you are not interrupted.

Zao’s wild ride arc start

Mayor Zao plans to use his unplanned visit to Parusa to find a new Battlesphere champion to fill Kalaw’s absence.
The meeting spot is on the other side of Tidal Gate (sigh…) - Zao refuses to go anywhere on foot, and his ship is landed there after dropping off Lilac and the team just moments before.

Stage 14: Tidal Gate

Same stage as in the base game, even tho technically you go the opposite way.

(Somewhere after Lilac and the team completed this stage)

After meeting up, Zao explains his grand plan - he has heard of a strong warrior training on the very summit of the local volcano, and he strikes him as the perfect new Battlesphere champion. He tasks you with locating the ‘warrior’, and convincing him to work for Zao. All on foot, as Zao refuses to get his shiny ship anywhere near the volcano’s smoke - at least he takes Kubo back to Adventure Square under the requirement that he drives the ship there.
>When asked about payment Zao proceeds to avoid the question.

Stage 15: Nalao Lake

(Before main heroes)

The fastest route to the summit leads trough Nalao Lake - at this point Merga’s forces are not yet under Serpentine’s control, and remain in their base forms. Serp-only enemies are replaced with other enemies from Merga’s army.

The boss is hotwired BFF2000, which Aaa attempted to pilot by themselves. Same fight as in base game’s Globe Opera 3, but Aaa screams more. After BFF2000 falls back into separate Beast parts, Aaa escapes in their Tunnel Driver.

[Alternate stage ideas]

Stage 16: Magma Starscape

Same as base game. 100%. Maybe the drill boss gets nerfed since he is way too spongy.

Stage 17: Diamond Point

After arriving at the summit Kubo quickly realises that the famed ‘warrior’ Zao spoke about is in fact Askal, the betrayer of Shang Tu. Kubo proceeds to retreat but is stopped by Askal, forcing a fight.

After defeating Askal, he decides in an effort to ‘win’ explaining Merga’s plan of raising Bakunawa back into the air. When that fails to leave as huge of an impact as he hoped for, he lets Kubo go.

On his way back down, Kubo contacts Millie with the news of Merga’s plan.
Millie states she needs time to dig out details on Bakunawa and it’s capabilities, and hopefully it’s current location. (basically until both contracts are done, as they can be completed in any order).

Zao’s Champion arc end

Kubo arrives at Adventure Square to find out Zao is not there - according to one of the locals, Kukri, he has just left in a hurry after meeting up with a purple water dragon and her friends. She also says Zao kind of just threw her a package and said to give it to a ‘black and white cat’ once they are back - and Kubo fits the description. The package contains a payment, few ZaoLand coupons, and a note saying that Zao actually no longer needs a new champion.

Ancient Dragon Relics arc

Millie calls Kubo over to her camp - using partial data from the Data Cores, recovered historical documents, and “other sources” she managed to locate one of the construction sites responsible for assembling Bakunawa project components.
Even better, said construction site seems to have direct underground train line to a whole undersea city from the days of Earth and Water dragons living together.

She asks Kubo to go there, and hopefully find something which can help them, or the heroes which seem to have the same goal, to stop Bakunawa - anything will do, from technical documentation to emergency shutdown codes.
Millie would love to accompany him, but due to personal reasons she refuses to elaborate on she can’t.

[This can change if a sprite artist would be willing to also draw her action sprites, in which case she will tag along as both playable and a follower]

Kubo takes the occasion to express his fear of deep water and drowning, but Millie ensures him that everything found to this day shows that dragon architecture is built to last and should be in perfect condition even now.

The entrance to the facility is located deep within the jungle, which recently took a massive hit from a battle happening between it’s trees.

Stage 18: Burnt Zulon Jungle

(Stage happens after main heroes dealt with Serpentine and recovered Syntax)

While sharing similar layout to the base game stage, whole jungle is burnt down from the bombs and fires which followed the confrontation between Merga’s and Serpentine’s forces.

Stage 19: Ancestral Forge

Once arriving at the location, the depth causes all communication with outside to cease - Kubo has to now find the way trough the place himself. Luckily it seems someone has already cleared the door puzzle letting him proceed to deeper sections of the facility.

While main heroes were looking for flowers and therefore took a route trough collapsed sectors and caves, Kubo instead goes trough more stable area of the forge, the actual manufacturing site and it’s connected habitats and offices. Therefore the stage is less stone, and more metal and machinery. It still maintains the ‘stone, lava and water’ aesthetic however.

In the facility Kubo recovers plans of several of Bakunawa’s components, specifically it’s lunar drill and FTL engines, as well as Data Core #6 (which seems very suspicious to him, as a recently ejected part of a starship should not be lying in a 100s of years old drawer).
At the end of the stage, he arrives at the station for the underground train and sets off for the city.

Boss of the stage is fought on top of said train, and is a souped-up version of Duality. Once damaged enough the double-sided dragon lands in front of the train, only to get destroyed by the impact.

Stage 20: Forgotten Dragon City - Atlantis

[or some other creative name]

A completely custom stage, map location is the underwater city thing one sees in volcano map after unlocking Gravity Bubble (which we skip)

(Same time as events in Gravity Bubble)
Arriving at the city, Kubo is amazed by the sheer size and design of the place - it rivals Shang Mu in the scale, with designs reminding him of his homeland.
Seemingly the ocean does not isolate signals as much, as he soon after manages to get communications with Millie going again. She refuses to elaborate on why a data core would be in an ancient dragon structure, but asks him to be very careful - the city’s defences might still be active after the sudden war that killed it’s occupants.

The city design shares a lot with Starbound’s Hylothl cities with heavy steel holding the water at bay, while wood and paper keep the inside warm and homely. Due to flow of time, certain connector sections between buildings are damaged, and require swimming between them. Kubo reiterates about his fear of deep water.

At the end of the level you find what looks like a final stand of several water dragons - bodies of which have long turned into feathers, but one of them remains clutching a Data Core #10. Millie refers to the dragon by name Lily (which she quickly covers by saying she saw that name on old statues), mentioning in suspicious details her heroism in the final moments of the war.

There is no boss for this stage. The minute of silence for the fallen is interrupted by blaring sirens, as the whole place shakes.
>Bakunawa has just been activated
The sheer energy of the water currents caused by it’s activation starts tearing the city apart.
Millie, in panic, relays Kubo the fastest path to the escape pods - the only thing that can get him out of the city.
An escape sequence starts (with scary looking but very forgiving timer), where Kubo escapes the slowly flooding city.

During the run, he asks Millie why would dragons ever build city so close to the launch site - as to which Millie simply replies “Do you really think they needed their watery ‘friends’ after the ship was done?”

Arriving at the escape pods, Kubo boards one of them which launches off just in time as the massive city structure falls apart. Kubo is visibly shaken by the whole ordeal.

Dragon Relics arc ending

So shaken in fact, that he is still not his normal self even back at the research camp. By this point it is also clear to him that they can do nothing to stop Bakunawa. Millie interrupts his sentence, telling him to look at the moon: Bakunawa is attempting to mine it, but it fails - it was way too far from it to mine it. She explains that the plans Kubo recovered point out that the mining laser has a very limited range, much worse than what it’s designers intended. There might still be time.

Normal ending

Kubo leaves the camp, in hope to find Maria. With her, he sits on the top of one of the buildings observing Bakunawa as it makes it’s way towards the moon. The ship’s blue lights seem to shimmer green at some point, but finally an explosion throws it off course and back to the planet. Everyone celebrates world being saved, and Maria gives Kubo a long bat hug. They take off to Shang Tu to get the report on the crashed ship and heroes who saved them all going.

Millie is shown looking at the events from the seclusion of her camp, holding the stack of data cores - her work was not done yet, but it would be a story for another time.

True ending

This ending is only available if you watch (and read) contents of all the cores you can obtain before the final stages.
By this point you know the story of Wayfinder, fates of three out of it’s four probes, and their perspective on Water Dragons and the Earth Dragon invaders.

You watch the remaining two cores with Millie, core #6 showing that Earth Dragon’s crash landing, and core #10 showing final moments of Probe Gamma, Lily - and that she used the moment she had to imbue it with piece of data which could change the tides of fate, were it needed once again.

The data core recovered from the city has proven to be very interesting. Outside of the usual video data and telemetry, it contained encrypted set of data defining a signal, which when sent to Bakunawa will disable it’s onboard AI drone. Such thing should stop the ship right in it’s track. Within a signal a video stream was also encoded, but only the ship drone can decode it.

As a last ditch effort, the team transmits the signal and waits. First Bakunawa goes dark, but suddently its colouring shifts to green as it violently moves back on course - almost as if it fighting itself.

Watching the events unfold, Millie offers Kubo one last Data Core to watch, core number 12, one not shown on the maps.
The truth is that the core was never ‘lost’ to begin with, it was always there in her hands.

The core contains a report like all the previous one, by Wayfinder’s final observer unit codenamed Omega. As soon as the video feed loads, it is obvious that the last probe was none other than Millie herself.
The report explains the events just after Brevon’s arrival - as Wayfinder fell, Millie for the first time in her existence was truly alone and free, with no external presence watching over her and providing orders. For once, she was the one to choose her path. Backup protocols she was equipped with instruct to locate the station’s wreckage and secure the data it held, but after that they state nothing - no “wait for orders”, no “shut down”, nothing. She decides that her obligation to her creators end with that, and that she will do all she can to aid the planet, and it’s people, where she spent her whole existence on.
Message ends with a note, that if it is not her who handed you the core, then she likely perished on this task - she requests to not dwell on the foreign world she came from, but to protect the one you already own.

Silence follows as Kubo makes sense out of all of these news.
Millie’s uncanny knowledge of the past, her ability to skip sleep and lift objects of immense weight, her dedication to the search for the cores, and all the other small clues that never added to anything before. It all made sense now.

Millie admits she kept her identity a secret all this time, out of many reasons logical and not. She knows the past not from research but by, in a way, simply remembering it - the memories are not hers, but she can still parse them as such.

She explains she cares not for her creators - they abandoned her and the station centuries ago, leaving them to forever wait for a word from their homeworld which never came.
She is however curious about the reasons for such abandonment - has the mission taken so long they didn’t need it anymore, have they forgotten about it, or maybe something had happened to them?

All she did to this point however was not some task given her by remote will, not some backup protocol set in place by her makers. She acted to save Avalice out of her own free will.

The final question is one she knows no answer to: she asks Kubo if he thinks her feelings are real, if he believes she is truly alive - or is she just merely a machine, one complex enough to simulate feelings and existence, but not truly alive.

Kubo answers what he believes, that she is equally alive as he and others are. That it doesn’t matter if her feelings are based in digital circuits since as long as she truly follows them, they are as real as any other. That he does not think of her any less knowing what she is. And that most importantly she still is, and will be, his friend.

But in the end, this truth is all she can offer now. There was nothing else they can do to delay Bakunawa. Their plan somehow failed, due to no fault of their own, but still it failed.
Only hope that the heroines aboard the ship will persevere and take it down for good.

She tells Kubo to go find Maria - if the ship gets stopped she will likely need someone to take her to the crash site for a news report. If the moon get’s destroyed and the world is set to fall into chaos - at least they will have one last moment of peace together.

Kubo leaves in hope to find Maria. With her, he sits on the top of one of the buildings observing Bakunawa as it makes it’s way towards the moon. Just before getting in the moon’s mining range an massive explosion tears off part of its hull and sends it falling down onto planet. Everyone celebrates world being saved, and Maria gives Kubo a long bat hug.
She then goes on about exciting new report she can make about the latest events… as well as few nice spots to spend a night together when that is done.

Millie joins them soon after - she admits that now that her objectives are done, she has no idea what to do with newfound freedom (in fact she likely expected to shut down after the task). She makes the decision to stick with her archaeologist cover for a while longer, as between the relics found on the adventure and knowledge of the past from previous units, there is a lot she can do in making the once revised history of water dragons factual again.
And also she needs a ride to Shang Tu.

The story ends on Kubo and the crew flying off aboard his ship towards the distant lights of Shang Tu, with the full moon shining upon the sea waves.

Roll the credits~

Bonus content:

Data core contents ideas:

Subject to change.
Italics in Wayfinder’s logs indicate glitchy text effect. Even with restricted AI the centuries of operation allowed it to, at least partially, think for itself. These are the result of such ‘deviations’ in it’s programming.

Data Core 1

A vaguely furry figure, whose details have been long lost to slow decay of the data, speaks about the ARS project. The greatest achievement of their era, a set of starships meant to visit closest habitable planets and relay the data back home. The Automated Research Stations are each equipped with state-of-the-art artificial intelligences, for both itself and 4 universal ground units meant to explore the surface directly.
Each ship can decide by itself on how to use these probes, as well as on their construction and looks.
The speaker mentions that they will not be around to see the results of this expedition - likely not even their children will - as even the shortest planned route will take over a century to finish, and just as long for the Ship’s signal to get back to them.

The last part of the recording is dedicated to whoever found it - be it a future colonist, a traveller, or maybe a being native to the world the station explored. A classic “by the time your seeing this we might be long gone, but our legacy lives on” thing.

Data Core 2

Core contains textual report following the station’s first activation.

>>Stellar communication array calibrated. Compiling report:
>>
>>Primary planetary analysys complete.
>>Providing information on target exoplanet #2:

Diameter: 9.31km
Orbital Distance: 151 million km .
Surface Gravity: 0.738017 G
Escape Velocity: 0.982 km/s
Axial Tilt: 23.782°
Atmosphere: 78% N2, 21% O2, 1%
Ar Surface Pressure: 102 kPa

>>Final verdict: Planet meets all habitation criteria.
>>Secondary analys indicates presence of possible intelligent life on the surface. Probe Alpha deployment underway for infiltration mission.
>>Awaiting orders from Terra and continuing observation.

Data core 3

Alpha takes look of an orange bird woman, living alongside the native bird population in a region that would one day become Shang Tu. While her plummage does not fully match the others (not all the details could have been observed from orbit), they still accepted her as one of their own. During her time spent near the villiage she got to enounter other groups of early avalicians, which held peaceful relationship with the birds.

Data core 4

Between all the stories told by the birdfolk, one struck Alpha’s (now known by locals as Vixy) interest the most.
It spoke of a group of fishfolk who inhabited the nearby oceans - while such a story could easily be grouped as myth, tales of metal cities and technology not understood by locals matched energy readings Wayfinder picked up every so often.
Birds have feared them since times immemorial, due to their draconic skills which were able to target ever an airborne bird, and as such never truly elaborated on them fearing that just mere mention of them would cause their return. By this point none of them knew where such dire fear comes from, but Vixy speculated an armed conflict must have occurred once in the past for it to hold such a grip even today.

Data core 5

Between stories of the locals, and orbital imagery Vixy managed to locate one of the water dragon settlements on the coastline.
Under guise of being a wandering scholar Vixy managed to make her way there, and get a basic grasp of the water dragon culture and society. While they did not wish to open up to a random bird, they seemed much more civilized than what the avian stories told about them. A society of both warriors and scholars, they excelled in bioengineering rivalling even that of Terra - taking on properties of multiple species of fish, their people were as diverse as the ocean itself.
She plans to remain there, hopefully gaining trust of the dragons to figure more about them, and why the other birds feared them so much.

Data core 6

>>Time since last reply from Terra: 274 planetary cycles. Worrying.
>>Sudden interruption of communications might imply obstruction on signal path.
>>Retransmitting last data packet at maximum signal power. Secondary transmission sytems considered for next transmission.

– Unspecified time later.

>>Unnatural power signature detected in planetary orbit. Closest match: Theoretical FTL drive.
>>Scanner array set to aim at unidentified object. Estimated course will enter atmosphere in 3 hours.
>>Visual observation of the target matches data from sister unit ARS Skywatcher (151LY from current location). No external damage of the alien vessel recorded.

Video footage of the Earth Dragon colony ship is projected, with it’s design being alike to Bakunawa based on a dragon, this time much more to classic depiction of such. It’s colouring matches that of Pangu, with white paint and blue details.

>> Priority update for unit Beta: Abandon all current tasks. Investigate anomaly.

Data core 7

Centuries have passed since Vixy made her last report.
Her replacement, unit Beta, took a form of a water dragon named Amelia. Up to this point she held a position of the water dragon lorekeeper, which gave her a perfect opportunity to join the investigation team around the crashed starship.
She recalls that the Earth dragons while acting corteous and friendly from the first meeting kept talking behind her back in their own language - one a water dragon should not understand, but which was quite easy do decipher with Wayfinder’s processing power. And it was nothing nice.
She plans on continuing her efforts on extracting information on the ship and the earth dragons themselves over the next years.

Data core 8

Another water dragon, looking much more like the modern depictions of them is shown. Unit Gamma, named Lily took over Amelia’s work after her unexpected termination. While the details are unclear, she believes her predecessor asked bit too many questions when she should have not.
Between the reports, an alliance was settled between both dragon groups - for getting access to the ship’s condensed power core, water dragons agreed to aid earth dragon’s project of reconstructing their ship.
Lily decides to stay on guard - she will not repeat the mistakes of the one before her.

Data core 9

Lily has secured several pieces of design documents on Bakunawa. While the main goal is to transmit them off to Terra, the plans themselves put a worrying light on a whole project. A lunar mining laser designed to be fired underwater and within the planet’s atmosphere? Construction so close to the water dragon capital that it will get damaged by the launch?
The questions pile up, but before she manages to decide what to do with this information, a violent blast shakes the ground - as people panic it becomes clear what just happened: Bakunawa shot half of it’s construction site, as well as an entire coastline.

Data core 10

The recording is short, and hastily recorded. Lily reports how negotiations with earth dragons failed, how they betrayed them with a fake peace meeting, and how they captured Merga and possibly killed their own princess just to have excuse to resume the assault.
But what they didn’t know is that Cordelia prepared a backup plan for just that - data packet that could stop Bakunawa from ever leaving this planet. While she hid one of the copies somewhere[time capsules, if implication was not clear enough], Lily managed to recover a copy of it for herself, and encode it into the data core she held.

As the video ends, she’s seen standing her ground with other water dragons exactly where you find her in the present.

Data core 11

>> Time since last reply from Terra: Too long.
>> None of the communication attempts succeeded. Both secondary laser array and radio antennas got no response.
>>They are all gone, aren’t they.

Rest of the data is considerably corrupted, but it’s clear enough to still make out.

>>Unnatural power si-----es detected in pl----- orbit. ------ match: Multiple FTL drives. ------------ not match known Earth Dragon design.
>>Multiple ------ flares dete—.
>>WARN: Critical hull damage sustained. Unable — maintain ----- orbit.
>>Priority update to unit Ome---- maintain cover ---- locate ---- cores ---- Use ---- freedom for good
>>Ensure this world ----- not meet the same fate as Terra ---- *static*

Data core 12:

Shown in true ending.

Zao’s Virtual Reality Arcade

A way to replay stages not present in the story.

An extension to ZaoLand, this hub area contains an VR arcade allowing anyone to experience adventures of the brave heroines who saved the world.
Kubo can play trough Bakunawa 1-5 stages here, as well as trough Palace Courtyard.
Original game’s versions of Airship Sigwada, Nalao Lake, etc. can also be replayed.

Some loose details and backstories

Kubo:

Kubo

Name: Kubo
Species: Cat (as there are no [non-dragon at least] hybrids on Avalice)
Description: Tech-skilled airship captain from a country outside the Tri-Kingdom area, coming to Shang Mu to find a future for himself. He is a caring person, always willing to help his friends and those he cares about. Spending time with friends slowly helped him get over his anxiety, which now comes back only so often.
During events of FP1 his airship got grounded after Sky Battalion blew most of the Shang Mu dockyards up, however by today he got it fully fixed and ready for flight once again. Some say he dreams of having wings like bats do, which led to his choice of career as an airship captain.
His main source of income are freelancer jobs, most commonly from Three Kingdom News, and from Millie.

Kubo’s Airship

Unremarkable on the surface, Stargazer is Kubo’s airship and home away from home. Unlike the ships common for the Three Kingdom region it uses jet engines instead of rockets - a much more energy efficient, but slower, option - which are an holdover from when it operated outside the Three Kingdoms, as before the birth of Kingdom Spiral these faraway lands had to depend on oil based power sources.
Alike the other ships, it can land on both water and solid ground, being equipped with landing gear for both occasions.

It’s weaponry includes plasma guns, missile launchers, and a frontal laser. Modified shield emitters allow it to ram into smaller objects if needed, at a major energy cost. All these modifications were added so the Sky Battalion incident does not happen again.

Millie:

Millie

Name: Millie
Species: Wolf (?)
Description: An archaeologist specialized in history of the water dragons and their culture. She has spent last several years in Parusa on an extended research expedition funded by Shang Tu museum. Being much stronger than she looks, she’s also known for her combat and leadership skills.
She has never disclosed her country of origin, but most assume it to be Shang Tu due to her archaeology degree obtained there. Not much is known about her research before that moment - almost as if she appeared out of nowhere.
Millie holds a big interest in specific set of artifacts which do not match any known Avalician culture, as well as one far away star system which has been recently discovered with her help.

Knowing Kubo for many years she is willing to do anything to keep him safe, even if she will never openly admit so.