Val and her mother are aboard an airplane, flying over an ocean. Suddenly, things get turbulent, and the plane quickly loses altitude. As the plane plunges into the ocean, everything blacks out. Val wakes up at a corridor with two mirrors beside her, one of the plane wreckage in the sea and another of a glimpse of heaven. Scared and worried for her mother, she instead turns her back and wanders into the darkness, eventually stumbling into a pit where she fall from an immense height down into Limbo, plunging into the sea and blacking out.
After falling, Valerie wakes up on a beach with no clue of where she is. Finding no sign of her mother, she wanders around a beach until she encounters a hostile spirit. Ambar, a cranky old man, appears but instead of warding it off lets it fight Val. He instructs her on how to use Virtue to cast magic and how to win a battle against spirits. Ambar takes her to his hut where Pelas, an enthusiastic young boy, is setting up a meal for Val, having found her earlier and sending Ambar to check up on her while he prepared dinner. Ambar and Pelas both tell Val that she is now in Limbo and explain a little bit about the tribes and Virtues. When asked about her mother’s whereabouts, Pelas replies that he didn’t see anyone with her on the beach, causing her to panic and cry out for home. The boy suggests that perhaps she could accompany him back to the Water Village to meet with his parents who might know of a way to find her and get out.
Pelas’s mother and father, though kind, are experts in marine biota and cannot offer much help. Realizing how useless they were in this situation, they began to panic. In order to make up for their inability to help, they instead give her a map of Alto Pyrenis and tell her to ask around the village, hoping that maybe one of the residents would know how to help her. They don’t. Disheartened, Pelas suggests they visit Ambar for another lesson in battle. Ambar gives her some equipment and tells her about the Founders and how they have taken control over all of the tribes. Seeing how late it is, Ambar escorts her to the Water Village where she can take a boat ride to the mainland to find a way home. Upon arrival, they find that the Founders are threatening the village with a message from the Trustee, who says that the researchers are late with their results and that “funds” will be cut off if they do not comply. Ambar steps in, saying that they cannot do this when they already have taken so much away. In a fit of anger, he attacks one of the guards, prompting the Founders to kill him. While the tribesmen look on in horror, the head of the guard states that as further incentive, some “funds” were to be taken right at that moment. The guards seize Pelas’s parents and a few other researchers and take them away.
The remaining villagers explain that the Trustee provides the village with “funds”- that is, people. If they do well, they release villagers they have captured and send them to the village instead of in a prison lab setting. Should they fail, they are instead taken away, with the tribe struggling to both complete research and provide for themselves. Pelas is heartbroken, losing both his parents and his mentor. However, Ambar reappears but as a peaceful spirit, claiming that Val and Pelas still have much to learn and his desire to help guide them kept him in Limbo. They want to rescue them, but the villagers are not of much help, stating that they’d prefer to continue researching and getting them back then. Val must then convince the villagers that their research can actually be used to help save the imprisoned villagers rather than simply using up all of their time on studying.
Once they are persuaded, the villagers begin working on a plan. Val and Ambar alone enter the Founders’ Lab, infiltrating it and freeing multiple villagers. Upon freeing Pelas’s parents and letting them escape, Ambar urges Val to explore what the Trustee was using the villagers to research. The lab, unfortunately was flooded by the Founders. Trapped, Val is forced to face the Trustee in battle. Upon his defeat, the Trustee is forced to come to terms with the plight of the Water Tribe, undoing his former ignorance, and the Founders thereafter abandon the lands of the Water Tribe, leaving the natives in peace to rebuild.
Amazed at the tribe’s liberation, Ambar urges Val to free the other tribes on the mainland. They sail to the closest region, the swamp of the Dark Tribe. There they find the tribe to be surprisingly well-off; with the wetland as difficult, toxic, and dangerous as it is, before the Founders the tribe found supplies scarce. However, Val and Ambar soon uncover that the tribe is in dire straits as they are nearly bankrupt, having relied almost entirely on the Founders and being discouraged from getting their own supplies through the machinations of the Banker. With the people having money extorted out of them, the people will soon starve, leading to a massive wave of organized crime as people begin to both continue to rely on the Founders yet distrust them, forming the mafia, who are also tied to the Founders. Your goal is to both defeat the mafia and the Banker, breaking their reliance on the Founders’ supplies while simultaneously alleviating the constant fear the Dark Tribe has for both its future and one another.
Past the marsh and through the mountains lies the desert of the Light Tribe, where the people seem to be living an ideal life free of any Founder influence, which strikes Ambar as odd. Upon asking the villagers, it appears as if they have no idea of who the Founders are or what they have done to the other tribes, instead remaining clueless of the outside world and denying that bad things are happening. Ambar and Val soon find that the villagers have been kept in isolation under the seemingly paternal governance of the Mayor. However, the Mayor has in fact brainwashed a great number of the tribesmen so that the disappearance of their children and goods goes unnoticed as they are smuggled off into far away lands. By making contact with the last remaining unbrainwashed villagers, they are able to reveal the Mayor as the corrupt man he is. Angered by this, the Mayor reveals a strange device attached to his arm. Upon activating it, an Ignorance, Deceit, and Envy spirit appear and appear to fuse with him, transforming him into a grotesque watery, angelic, and demonic creature that Val must defeat in combat. Fearful of what this could mean for the Islanders’ future, Ambar urges Val to continue to the lands of the Fire Tribe, where defeating the Founders may lead to an island-wide revolt.
The Fire Tribe should have been willing to help, with the majority of the tribe being proud warriors. Instead, Val and Ambar are blocked off from reaching the village at every turn by the local militia. The soldiers have been enlisted by the Founders to guard the region against a rumored uprising while the Resistance led by Etanoli has been leading guerilla attacks. However, the Founders have been planning on the rebels’ attacks on finishing the tribe off once and for all- Val must quench the rebels’ wrath and break the General’s hold on the region.
Unlike the resentful Fire Tribe, the Nature Tribe instead decided to live in peace with the Founders. However, the nonviolent approach of the tribe has led to the destruction of the forest they love. Rife with violence, the people have fallen into despair and despondency where they feel helpless to do anything but watch as the Founders destroy their home. It is up to Val to stand up to the Warden and lift the people from their hopelessness into action.
The Ice Tribe is by and large a proud people bound by honor and the desire to be right, a trait that was noticed by the Founders. The tribe was then tricked into being indebted to the Founders with a deal that they could not fulfill. The tribesmen must provide enough resources as tribute, but it is sabotaged annually and thus they are unable to fulfill the requests of the Founders. Val must either stop the sabotage from occurring or convince the tribe to give their pride and honor code for the sake of their survival. Upon doing so, the Judge will attack the player, fusing with Fear, Wrath, and Malice spirits.
Everyone is smiling in the subterranean world of the Earth tribe. They all look so cheerful working themselves to the bone in the mines that Anbar and Val do not notice them starving at first. Despite the cheery attitude in public, the Earth tribesmen of the lower classes are miserable as the Founders used the custom of lending a hand no matter what to heighten the already-present class inequality. While the rich are free to spend extravagantly on luxury goods and donate occasionally to the local charity, the poor are so embroiled in their own financial woes that they are spending more time working in the mines to pay off their generous lifestyle. Defeating the Overseer will free the poor and restore balance.
The Thunder Tribe, for the most part, no longer identify themselves as such except for the old and stubborn, and even then only in private. With the Founders in places of power, the Thunder Tribe has been turned into the workhorse of the Empire by using their desire for success against them; in order to be successful now, all Islander culture must be abandoned and replaced with Founder beliefs. Val must stop the reeducation of the students by urging them to find their own dreams rather than following the expectations of everyone else. In overthrowing the Principal, their identity is restored and they can be true to themselves once more.
The village of the Air Tribe, set atop the Cloud Mountains, appears to be thriving in spite of the presence of Founder soldiers with the various art guilds showcasing their talents throughout. Despite this, the artists themselves are clearly in trouble: the guilds have been manipulated into an envious rivalry against one another where sabotage and conflict run rampant. The Gallery Show is coming up, where each guild will be judged based on their work and the Curator will choose who gets the Founders’ patronage for the upcoming year- that is, who will be supplied this year with food, money, and other necessities, and who will starve. Val must break the jealous rivalry between the factions and get them to work together instead. In restoring balance to the Air Tribe, the Curator fuses with Greed, Sloth, and Deceit spirits.
The rebellion culminates in the surrounding of the Founders’ lands in the center of the Island, once the Capital. However, a barrier has been set up in the plains, inaccessible to all but Founders and Metal Tribesmen. The plains are barren, with a few Founders’ forts dotting the area thanks to the Spirit Tribe genocide and the betrayal of the Metal Tribe. Val meets the last unassimilated Metal Tribe member and must help her walk through the regrets of her past in order to break into the Capital. The miniboss, the Prophet talks of salvation for the Founders in the creation of new and brighter empire in a world far off, unsettling the heroes.
With the rebellion at its closest, Ambar is worried of the Founders’ progress on the technology and what their motives are. Wandering off into the plains, Val is captured and imprisoned within the Capital by the Founders in hopes that they get some information out of her. She escapes and must battle her way through the Timeless Ruins of the deported Order Tribe as well as the Starscraper of the sealed-away Chaos Tribe, learning about hope and patience as the rebellion needs it. At the top, she faces off against the Scribe, who talks of the Founders’ troubles in running out of resources and the desire they have for more, causing them to create a portal to Earth where they can have more. At their defeat, Val must broadcast a speech to the rebellion with the choices she sends affecting her Virtue for the final battle.
With the final dungeon, Val must go alone in fighting through waves after waves of spirits in the Imperial Palace. There she faces off against the one who started it all: the Founder Emperor, His Imperial Majesty Tredecimus Vitiae. In building a portal to Earth, the magic of Limbo renders their technology useless; however, since spirits are inherently magical, the Emperor starts the fusion project so that supersoldiers can make takeover of Earth simple. He then fuses with 13 hostile spirits of all the vices and morphs into a hideous monster blocking the way of the portal. After his defeat, the Founders all flee, but the portal is finished charging with only one possible use. Val must decide whether to return or stay, and then the epilogue happens.
Depending on how many of the hostile spirits you defeat (there is a set number per area) and which choices you make in the final chapter, the epilogue can come out differently.
If she stays, Val becomes an ambassador for the tribes. Though the Emperor is defeated, his minions still control the Founders Empire elsewhere in Limbo though its hold is falling apart. Some Founders who converted to Virtue decided to stay, though others couldn’t last and left for other lands. The outcome of Alto Pyrenis as a whole depends on how many hostile spirits she has defeated. With a few defeated, the Islanders are left alone by the Founders but the presence of so many hostile spirits makes development difficult, leaving the nine/ten tribes isolated and disunified. The Founders who wanted to stay were kicked off the island due to conflict, leaving them to practice Virtue elsewhere. The Imperial forces attack the weak nation every now and then, but it still remains autonomous. With more defeated but not all, a weak federation forms with Val at its head, still prone to conflict but less so than before. This time, the converted Founders are instead integrated into the remaining tribes, and the Empire leaves the island alone. With all of the spirits defeated, the tribes are unified under a strong democratic government with Val as its eventual head. The new nation is strong enough to influence the Empire into letting the deported Chaos and Order tribesmen return.
If she goes home, she wakes up amongst the wreckage of the plane floating in the ocean; if she defeated only a few hostile spirits, her mother’s jacket can be seen floating in the water, implying her death followed by Val crying and paddling away. With more saved but not all, Val will just look off into the ocean, waiting before rowing herself away. This ending is open to interpretation as to what Val’s mother’s fate was. With all hostile spirits defeated, Val wakes up and sees her mother unconscious next to her, checking her vital signs before rowing off into the distance.
In both cases, the closing scene is a childish scribble of Val and all of her friends.