Main protagonist is a white mage and his best friend is a knight; the mage is kinda based on Arc, the knight is kinda based on Leo. Their kingdom has been hunting down Eidolons to destroy them, believing they are destructive beasts. However, Arc prefers to study instead of fight and his research has led him to wonder if Eidolons are peaceful. While Leo is loyal, he's starting to share his doubts. When they speak to the king about this, the king seems to agree with them that it is worth looking into, and assigns the two to find an ancient village reputed to know much about Eidolons, and discuss with them if the creatures can be reasoned with. The king gives them a royal signet ring to carry as a sign of peace.

Since they're going to have to be undercover, the two are sent alone. They hire a thief and mercenary to guide them through unfamiliar regions; this guy is mostly based on Shadow with hints of Amarant and Edge. The two also learn that outside their borders, their kingdom is seem as warmongering and tyrannical. The group finds a forest and a girl caring for an Eidolon; she's primarily based on Rydia. She and Arc take a shine to each other and she eventually leads them to her village. The village Elder tells them yeah, Eidolons are totally peaceful, and the group hangs out there a bit watching the villagers interact with the Eidolons.

An army razes the village and kills the villagers and the Eidolons. Leo duels their leader, a Seifer/Ravus type who had earlier been established as a rival. He reveals the signet ring Leo was given was a beacon to direct them to the village, and they're there under the king's orders; the inhabitants of this village are Summoners, they can control the Eidolon. Arc tries to help Rydia and the Elder escape but the Elder has already been wounded and Shadow helps them flee. The party regroups Rydia confirms that she and the other villagers were Summoners, though she's never been able to summon much of anything, only the weakest of Eidolons.

They agree to return to the kingdom to confront the king, and they stow away on Seifer's ship and take him hostage. At the kingdom they disembark and come before the king, claiming Rydia is their hostage. The king confirms they were used; the Summoners are the true enemy he's been seeking to eliminate, but they're a cautious and suspicious lot, anyone sent to find them had to seem sincere in their efforts to understand them and the Eidolons. With it being obvious that the ruse is over, Leo refuses to serve the king any longer and draws his sword against him. Shadow insults him as a feeble old man, and the king laughs, stands, and raises his cane; with a flash of light, he transforms and reveals he himself is an Eidolon, Odin.

The duel with Odin spills into the courtyard, Leo and Shadow barely defending against him; Seifer is watching, unsure if he should get involved. Eventually with Arc's encouragement, Rydia attempts to summon and conjures the spirit of the Elder, who is revealed to be Ramuh. With Ramuh's help, the group is able to destroy Odin. Before the summoning ends, Ramuh tells Rydia she isn't the last Summoner, and fades away. Seifer picks Odin's sword and declares the others traitors, and they flee as guards converge. The group decides they must find the other Summoner Ramuh told them about, and protect any remaining Eidolons as they can. With the king dead and no other members of the royal family, the nobility appoint Seifer as regent; he's pleased with his new position, but clearly conflicted.

In a post-credits scene, a cloaked figure muses on Odin's destruction. It is a setback, but their plans are still progressing well. And they have other minions that can be deployed. The film ends as the figure steps onto a balcony where various beings are building a massive machine that looks suspiciously like Alexander, and the camera pans out to reveal they're on the moon.