Pampered prince Luke fon Fabre is bored. After being kidnapped seven years ago his father has confined him to his place. But after a mysterious woman appears and attacks his master, Luke is blown away from his home.
Luke and Tear realize they're in the wrong track home after discovering they're in the Malkuth Empire. To make matters more complicated, they run into the supposedly missing Fon Master Ion. What other surprises await them?
Luke and Tear are taken into custody by Jade and asked to help them out-which could help them get home. But when they're suddenly attacked, things take a dark turn and Luke finds himself with blood on his hands.
After reuniting with Anise and Van, they're nearly back home. But they;re stopped once more and wind up in the place Luke was found seven years ago after his kidnapping only for him to be captured once more.
On the ship home, they're attacked by another Oracle Knight and afterward Luke's body is suddenly taken over. Van finally reveals the truth behind his confinement and the power he holds.
Luke and his group get ready to head out on a mission of goodwill, but find out Ion has gone missing. Now with their plan complicated, they head underground to make their way to the mining town. But what dangers lie in wait?
At the Zao Ruins the group faces Asch's forces. But before they can get answers, the ruins begin to crumble and they get away. With Ion safe, they continue their journey to meet up with Van but Luke's words cause strife.
The group arrives to the mining town and before they can begin investigating, Tear is taken away for her own mission. Going deeper into the mines, Luke finds Van and readies to use his power. But has he been led astray?
Luke learns the truth of his existence and isn't taking it well. Meanwhile, the others try to find a way back to the Outer Lands but Tear decides to stay. Through Asch's eyes, Luke learns more about his creation.
Tear and Luke learn about the Closed Score and what has been prophesied. They return to the Outer Lands and meet up with Guy. But when Jade appears with troubling news, they must act quickly to save Ion and Natalia.
In Jade's hometown, the snowy city of Keterburg, his sister Nephry tells Luke about a tragic event that took place there. It is deeply connected to Jade's past, Dist of the God-Generals, and the secret of Luke's birth.
While waiting to get into the Malkuth capital the group is attacked. Guy's curse slot activates and Luke learns something troubling about his best friend. But there's little time to settle when talk of war begins to stir.
After rescuing the last few citizens of St. Binah, the group stumbles upon the first signs of war as two armies begin to fight. Shile trying to demand a ceasefire, Mohs appears with claims that could change everything.
The group makes their way to Belkend to see if there's a way to stop the Outer Lands from deteriorating. There, Guy meets with Van and breaks their pledge. But does that mean the group can trust Guy or is he a spy?
The entire Outer Lands collapse - Luke insists the king of Kimlasca and the Emperor Peony IX of Malkuth be informed of this horrific event, but Natalia is scared to see her father again. Just then, Asch shows up before Natalia.
Before they can set out, Van and his knights attack. He reveals his plan to create a replica of the world to escape the fate of the Score. With little time, Luke and the others must make their way to the core before him.
Despite Tear's condition, they decide to continue with their mission. With each Sphiroth she takes in more miasma. Will she be able to hold out until the end? Then, a match with Van points them in their next direction.
Curious about what Asch is after, Luke and Tear set out. Reuniting with their friends, they learn that Dist has escaped and with him, Mohs. Before they can investigate further rumors, they're betrayed by an ally.
The group finds Asch and learn that Van is still alive. Now that he's absorbed Lorelei, what does it mean for the future of the Outer Land? Then, an encounter with Dist leaves them facing a newly empowered Mohs.
Luke pushes Asch to reunite with his parents only to upset him further. Then, as the threat of the miasma returns, the group seeks a way to stop it. But their options look dire.
The group go after Asch in the Tower of Rem but before they can talk to him, Dist attacks. After the battle, they seek a solution that won't risk the replicas, but the only other choice could mean Luke's biggest sacrifice.
Natalia learns about her real father and must decide if she wants to continue fighting. But with everything resting on their ability to stop the Planet Storm, they must all push forward.
The group plans to make their way to Eldrant with help from the Malkuth army. While preparations are made, they take a trip to Daath where they run into Asch who pushes Luke to prove himself.
After landing on Eldrant, the group makes their way to catch up to Asch. When reunited, the two are suddenly transported away. While the others face the God-Genderals, Luke and Asch face their own problems.
Van tries to fulfill Yulia's Score by annihilating the original people and creating a new world with replicas. Luke and his party battle against his former master, who utilizes the power of Lorelei, at the deepest core of Eldorant.