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The story of Mobius Final Fantasy takes place on the planet of Palamecia where the prophecy about the Warrior of Light keeps the world going. It follows an amnesiac Wol who has forgotten his past and came to Palamecia as one of many candidates for the fabled "Warrior of Light".
As an amnesiac man Wol arrives on Palamecia on a string of light, a mysterious voice, introducing itself as "Vox", speaks to him, telling him about how his ties to the past are no longer valid in the world he is now arriving and speaks little about the nature of the world itself. The man wakes up finding himself in a strange world with a sword at his hand, many other men beside him. Vox then speaks of a law of Palamecia: "None shall remember the names of those who do not fight", forcing the man into battle of incoming monsters. The voice then asks them for their names, and surprised by how many share the same says that their name carries a special meaning as it is the name of a hero foretold to bring hope to Palamecia: the Warrior of Light, who will be one of the men who has just arrived as it is said so in the prophecy.
Considering the new arrivals "blank slates", Vox calls them Blanks. He then advices the group to go north and when Wol wonders what is there, an armor-clad man appears and says to follow the voice's words as it is useful most of the times. Vox then introduces to them a new law: "Your mettle is constantly being tested." As Wol continues his journey he comments on how everything feels like home to him despite his memory loss.
In Plains of Cornelia, the man sees a struggling moogle and is encouraged by the armor-clad man to help him, citing a law of Palamecia. He then introduces himself as Garland and that his role is temper any Blanks that show prospect of becoming the Warrior of Light. Garland states that all moogles share a common mind and saving it will make all moogles feel indebted to him. Pushed by the armor-clad man into help, Wol saves the creature that introduces itself as Mog that vows to protect his new "Master", while saying "kupo" a lot, startling his savior. Mog then takes Wol to the Runic Temple at Plains of Cornelia and after a series of battles arrives at the Intercrystal and beckons his Master to touch the rune crystal. An image of a young woman appears in the rune crystal and Mog introduces her as Princess Sarah. The moogle praises Wol's growth in combat and the Princess says she senses the same. When Mog speaks of how Wol rescued him from the monsters the Princess recalls a piece of prophecy: "For he shall walk with a moogle not behind him, but at his side". The Princess then states if Wol will vow to fight for the people of Palamecia, then the royal line of Cornelia will aid him on his journey, but he must choose this path, which he hesitantly agrees to.
Princess Sarah then bestows upon him a boon of House Cornelia and expresses her interest in meeting him someday. Mog explains that the Princess is in a far away place and that she has given him the power of teleportation which Wol states to sound familiar to him. As the two travel to Castle Cornelia to use the teleport stone to close their distance between them and the Princess, a strange light dances around Wol. The Blank thinks that Vox is keeping tabs on him, but the time stops still and a female voie speaks up calling his presumption an insult. The light then transforms into a tiny wingeg girl who introduces herself as Echo and congratulates him for being chosen and states that she will be his guide, but the man impolitely refuses. Wol comments on Echo's attire, but she shakes it off saying that only he can see her and she disappears. After the time resumes the Blank asks Mog about "any Echo" and he says that she is a field faerie who offers guidance to travelers and can lead others to great treasures, but sometimes at a great price. As they continue their jorney to the Castle, Mog says that the world is slowly dying because of Chaos and his monsters as he strives to turn everything into disorder and destruction.
Along the way, the two meet Garland who asks Wol of he spoke to Sarah. Commenting on the armor-clad man's lack of manners, he says he did and Garland warns him about women, but Mog says to ignore him as he is a heretic and Wol should follow the prophecy. When asked about the Princess's role in the prophecy, Mog starts to say something about her and the Warrior of Light and Garland tosses him aside, saying that not everyone needs to bauble about the prophecy. Vox the speaks up and orders Blanks to kill Garland. As he continues on his journey, Wol's smell perception changes and starts to smell mold. Wol complains about how difficult is to reach the Princess and Mog says that the prophecy states that his journey would be long and perilous before they would meet. Wol and Mog finally arrives at the ruins of Castle Cornelia where the moogle shows the man the painting of Princess Sarah and Wol comments on its old look. In thoughts he comments how the painting stinks to him and decides to leave the place quickly, feeling he would rot there. Wol then approaches the teleportation stone and as he touches him, Mog informs him it will take him to the Crownforge. As he travels there, Wol thinks about how talking with others makes him grow "attached" to Palamecia, although he does not know if it will be for better or worse or anything for that matter.
When they arrive at the desert, Mog tells Wol about an old Palamecian legend according to which royals where driven away from their castle and traveled the sands of the desert struggling to survive, yet that struggle made them stronger. Using the legend, the moogle encourages his Master to also travel the desert and get stronger, but Wol comments on it being not a very smart idea. Then Mog frantically starts to spin around him and when asked what's wrong, he admits it is a first time for him to be in a desert but is not worried and once again calls on the prophecy saying they need to find the Runic Temple and receive the blessing from its crystal. As they travel, Mog recalls hearing about keys hidden among the sands. With Mog's help, Wol finds a key in the Temple Fringe and when asked about the prophecy he states that according to it he needs to find four keys in order to gain access to the Runic Temple. Wol comments on how quick such a specific information came to the moogle, and Mog explains that as all moogles have a common mind they share their experiences and knowledge with each other and encourages his master to ask him questions.
After finding three keys, Mog teases Wol about a big Blank gathering which he think his Master will enjoy, but doesn't specify what he exactly means by that. As they travel in their search for the fourth key, Wol meets a couple of Blanks who reveal to him that the Wol Namesgiving Tournament where Blanks fight for the right to claim the name "Wol" and say that the main prize for winning it is a key to the Runic Temple.
During the journey through the Runic Temple, Wol and Mog come across a Lich enemy several times. After each defeat, Mog alludes that a friend is supposed to protect the Warrior of Light in battle. In the third fight, Mog even attempts to fight, but Wol pushes him aside, continuing the fight. After the the fourth and final battle, Mog insists that he delivers the final blow. Wol agrees aloofly. Mof then flies into the Lich in a killing blow, but is hit by the Lich in return collapsing to the ground. Wol, initially thinks that Mog just took a hit, but notices his pom-pom losing its glow and picks up Mog in worry. Mog wakes up weakly and confesses that he was supposed to sacrifice himself so the key could reveal himself to the Warrior of Light as told in the prophecy.
Wol tries to deny this saying no key is around telling Mog to get up. The key appears, confirming the prophecy to Mog's happiness. Mog is happy that this meant that he is considered a friend to Wol and he will always be a friend to the moogles. Wol accepts this but asks that Mog keeps some of this happiness for himself. Mog says he can't since it's a law of Palamecia. As a final request, he asks Wol to hug him, Wol complies and embraces the moogle. Mog is so happy that this is something he can keep for himself bragging that the other moogles would be so jealous. Mog then dies in a flash of light and the light dissipates into bubbles into the sky. Wol punches the ground in grief for his fallen friend.
Garland approaches Wol shortly after Mog's death, in order to lead him to converse with Princess Sarah and to the next Teleport Stone. When Wol questions him on his role in the prophecy and the unfolding events, Garland explains that he had refused to side with either good or evil, and was declared to be a heretic as a result. After taking off his helmet to reveal his face to Wol for the first time, Garland warns him that should he fail in his quest, he will simply find another Blank to use for his goals.
Garland accompanies Wol to Princess Sarah's castle, while telling him not to lose his heart to her. When Chaos mounts an assault on the castle, Garland travels with Wol across the battlefield, offering advice and observations as they watch countless Blanks throw their lives away in battle. After Wol is successful in battling Chaos and driving him back, Garland takes him to meet Sarah face to face. There, Sarah reveals that the final part of the prophecy of the Warrior of Light states that after defeating Chaos, the Warrior of Light is destined to wed her. She explains that she had always been worried about that portion of the prophecy, but after meeting Wol, she would be happy if it were him. Although he initially allows them to talk alone, Garland interrupts, insisting that it's time to move on. When Sarah asks Garland for his name, he refuses to answer, and leaves without speaking to her. When it comes time for Wol to move on to the next region, she declares that she will wait for him to return. Shortly after this, Garland parts company with Wol, stating that he's held his hand for long enough, and that he'll need to manage on his own for the time being.
However, Wol is surprised by Sarah meeting him at the Teleport Stone, stating that if she is going to have to wait for him to defeat Chaos, she would rather do it by his side than at the castle Though he is initially taken aback, Wol accepts her as a companion, and they use the Teleport Stone to leave the region together.
Wol ends up in a "world between dimensions", where Sarah is not with him and he fights through a series of trials, because Vox wants to see if he is worthy of vying for the title of "Warrior of Light." He succeeds, and while Echo tries trash talking Voice, it turns out Vox can hear her too.
Wol then moves on to a Valley-like area, where he is again with Sarah, and they make their way through to Mogheim, a Moogle village. While Sarah stays behind, while Mowg guides Wol through the land while he's fighting through, confident of the magical barrier surrounding the village. After noticing he has grown significantly in power, Chaos later comes after Wol, making him rush over to Chaos' general direction, but Mowg tries to hold him back, saying his safety is more important. He then gets a message from the other Moogles and tells Wol "they'll hold it off", though Wol is dubious. Confirming his worries, Mowg later says they're declaring goodbye. Realizing he's targeting Mogheim, Wol gets disturbed because he doesn't want more Moogles to die because of him.
Wol finally intercepts Chaos, but not before Chaos kills several moogles who attempted to delay him. He then proceeds to seemingly shoots a fireball at Wol, only that he wasn't aiming for Wol, but rather for Mowg, killing him as well. Heartbroken, Wol realizes that Chaos is trying to break him with the despair of his friends' deaths and refuses to fall victim to Chaos' dirty tactics, then summons Marilith in order to stop him. After Marilith is defeated, Vox teleports Chaos away. As he is left alone on the battlefield, he looks around, asking for Garland, for Vox; for anyone, to tell him what he should do next.
Sarah then reunites with Wol, unconsciously carried by Garland. They then head to land's border, where they see an island in the sky. Wol wonders what it is, and Garland says that as soon as he arrived, he was destined to go to that place. Wol heads to the teleport stone, alone, but not before Sarah gives him a tied up yellow handkerchief. Noticing a light in Sarah’s heart that no one else can see, Wol heads to the island, thinking on what it means.
Arriving on the island. Wol is greeted by a Moogle who says that his master is waiting for him. Heading up to the top of the plateau, an old man is sitting on a throne. He then beckons Wol, bidding him to walk with him down the path and revisit the past. Calling himself Cid, he reveals that is the first Warrior of Light – Wol’s predecessor.
Going through the land, it is revealed that long ago, there was a village called Palamecia. Cid and his younger brother, Mid, were two youths who were close with a girl named Sarah. A noble called Chaos one day called for Sarah’s hand in marriage, but she refused, as she was in love with Cid, though only Mid notices it. Angered, Chaos cuts off the water supply of the village, and everyone starts to die of thirst. To save the village, Sarah agrees to the marriage. However, this was not enough for Chaos, as it was clear that Sarah was not truly in love with him.
Eventually, a figure named Voyce (who is Vox in human form), approaches Lord Chaos and informed him of rumors that spread about him around Palamecia, and suggests that if he wants to win lady Sarah's heart, who has feelings for a young village swordsman, to organize a tournament in which he would best him, gaining the woman's favor. Influenced by “Voyce”, Cid enters the tournament to save Sarah.
Fighting through the first few participants, Cid eventually gets suspicious, as it seems that the participants are losing on purpose. Sending Mid to investigate, a while after, Cid finds Mid’s dead body, murdered by Chaos’ men, as had found out too much. Enraged, Cid goes after all of Chaos’ men. Eventually, the only match left is between Cid and Chaos. Knowing Cid is a threat, however, Chaos orders his men to chase down Cid and beat him until he is weak enough that Chaos’ victory is guaranteed. Though Cid defeats countless enemies, they eventually whittle him down, and beat him until he is barely able to walk, confident that he would lose to Chaos in that state.
At the same time Sarah is on a bridge, about to commit suicide, thinking that if she dies, all of this needless suffering would end. Cid stops her, and says that he would bring hope to this village. Vox then announces to the village that Wol would save them, kill Chaos and deliver them from this crisis – and as the villagers cast away their despair and start to gain hope, Cid sees their hearts light up as one – thus marking the birth of the Warrior of Light.
Before the fight, Sarah gives Cid a protective charm, the same one that the current Sarah gave Wol. Backed by the rest of the village, Cid duels Chaos and, albeit losing an eye, kills him. Chaos’ body flies over the edge of the cliff and the villagers celebrate. But unbeknownst to them, Chaos’ body sinks into the Earth in a pool of darkness. After that, the village was continually attacked by monsters, said to be born of Chaos’ evil soul. They were said to be Chaos’ curse, but as time passed the monsters that attacked Palamecia were just called “Chaos,” after the evil noble that had supposedly caused them to appear.
After hearing the story, Wol finds out what the Warrior of Light really is: A Warrior who brings hope to the people of Palamecia in a period of crisis by defeating Chaos. While every time Chaos is vanquished, a brief period of light begins, but Palamecia is destined to always fall again into darkness. When despair falls again, new warriors from different worlds are called, without memory of who they were or where they came from, to Palamecia, in the hopes that one of them would be the one to become the new Warrior of Light and defeat Chaos. As such, the cycle of Warriors of Light and Chaos continues in a spiral. Sensing this, Cid sent his Sarah away to a faraway world to protect from the danger of Palamecia, with the letters spread throughout the story belonging to her, who still sends him love letters from another world.
The sixth chapter then shift focus onto a different character, the heretic sorceress Meia. Known as the “witch of heresy”, she is being pursued by the summoned beasts of Palamecia as she is branded with the label of heretic, and is forever doomed to be chased because her existence is a threat to the Palamecian rule. She is also guided by a manifestation of Echo who is colder, but still represents the will of Palamecia. Fighting her way through, she defeats the summoned beasts one by one. Exhausted in the end, Meia is about to give up as a summoned Beast is on the verge of killing her, but Wol comes in with Echo and saves her.
Wol’s entrance reminds Meia of the time she was saved by a previous “Warrior of Light” candidate, much like Wol. This memory conjures up an illusion of this man, who is called Swordsman. This illusion serves as their enemy as they navigate through this realm, and the use of his appearance is intentional: to torment Meia by making her recall her painful past.
It turns out that the Swordsman and Meia used to be lovers, but the problem was that the prophecy states that the Warrior of Light will defeat chaos and marry the princess, Sarah. Aware of this, Meia tries to distance herself from the warrior, but he persistents, and convinces Sarah to acknowledge his love for Meia, thus breaking the prophecy. Believing that anyone with the light of hope in their hearts is a Warrior of Light, not just one chosen warrior, he says that he will find a way to solve the crisis of Chaos without relying on it by come up with his own answer and a new kind of hope, not the hope offered by a prophecy. Vox does not approve, and he plants suspicion towards the warrior and Meia in the minds of the other Blanks, causing them to band together against him, saying that to defy the prophecy is heresy and they must kill Meia, the reason for the heresy. They are cornered at the same bridge Chaos was killed at in the past and, after a brief altercation, the two are cut down and thrown into the same river as Chaos did, but end up floating into the stream. Meia says she would have been content to simply float away forever together, but something brought her back, as she eventually washed up on the same shores as the blanks, having become a new Meia who was now branded the Witch of Heresy.
After being forced to relive her past, Meia and Wol arrive at the place where the illusion awaits. Meia comes to peace with her past thanks to Wol’s encouragement and the two defeat the illusion, which fades away in peace. Wol thinks about just obeying the prophecy, but the two agree that the fallen warrior was right, agreeing that anyone with the light of hope in their hearts can be the Warrior of Light, even the fallen Meia. Hopeful, they move on to the next area together.
As Wol is being transported, he recalls how Vox tells him how his name is special, as its the name of the Warrior of Light that will save Palamecia. However, as there are many other blanks who bear the same name, Wol wonders why him, and not any other blank with the same name.
Wol and Meia arrive and are greeted by Vox. He reminds Wol that his name is special, saying that he would be bothered if Wol were to sit still and die in obscurity as the other blanks are destined to. Seemingly not caring about Meia's presence, he asks Wol if he considers her a dependable ally, and Wol responds that she’s just someone who brought him into the mess. Wol then asks why he instead of any other blanks. Vox then tells him the difference – Projecting a vision of the other blanks and Moogles cheering him on, while small lights shine in their chests. He explains that such light of hope was brought about by Wol’s strength and victories through Palamecia are what sets him apart from the others, and what makes him the Warrior of Light.
Telling Wol to go forth, he then finds himself in front of a crystal. Vox is essentially showing his journey to the rest of the world, and Wol sarcastically asks him about the time he said he didn't saw the light in him, and Vox responds that it was an encouragement and that he had found that light. He then transports Wol, sending him to relive his first moments in Palamecia. As he comes back to the real world he is then forced to defeat more enemies to inspire the people cheering him on. After he find several crystals and defeats chaos multiple times, Vox then continues to summon enemies for Wol to defeat, as Wol mutters his situation as he goes on to kill them.