The Mana Temple is a complex which was built around the Mana Tree. Several years before the story begins, this is where the man named Vandole arrived after crossing the Sanctuary to claim the power of the Mana Tree, to use its power to form the Vandole Empire, ushering a dark age through the unnappropiated use of Mana. Several years later, despite his apparent defeat, Vandole resurrects as the man named Julius, and begins anew a quest of an odd purpose. However, a hero rises once again to shatter his evil plans.
The protagonist and a friend, after a long journey, pursuit the resurrected Vandole through the Sanctuary. defeating the guardian of the sanctuary on the way. The Hero and the Heroine arrive to a temple in the depths of the Sanctuary, where Julius was awaiting for them.
After traversing the temple, they encounter one of Julius' shadows, and after a brief conversation he warns them that ahead lies sacred territory that no one except Julius, The Divine, can traverse, considering him a god. The Hero laugh to this nonsense, and yet the shadow of his master claims that he is above other humans, for Julius' heart does not waver. The shadow questions them of the righteousness of their deeds, asking them if they were doing the right thing by wanting to stop his master; asking them if they were fighting for the right people. The shadow summons the heroes' friends and forces them to confess their sins.
The shadow then summons Bogard, and tells them to listen to what he hides in his heart. Bogard confess them that he gave his wife to the Sanctuary, knowing she would never return, which the shadow says this to be his true face. With this, he then summons Lester and Willy, controlling them, and demands to reveal their sins.
First, Lester says that when his sister was taken by the soldiers, he felt not only sadness but also relief for being freed from her oppressive love, which makes Julius' shadow consider him a cold-hearted person. Soon, Willy says that when the Mana Village was attacked, he abandoned the villagers and their leader, which makes the villain call him a coward.
-In the Hero's story, Julius' shadow then demands that the Heroine confess, which causes her to say that at Consul Hermann's house when she first met the Hero, she envied him for his happy life with both parents. The shadow remarks how the Heroine had always wished the Hero was in her place.
-In the Heroine's story, Julius' shadow makes the Hero confess, who says that when the soldiers took him as a slave and took all his hope, he hated the Heroine for appearing in his life, and that if it wasn't for that, he would still be happy with his parents. So, the villain makes fun of his resentment for taking him away from his family.
In both stories, after showing what goes on in the hearts of their companions, Julius' shadow asks the protagonist what they think about it, but the other one doesn't respond and seem to hesitate. Using his magic he controls the allies to rise up with their weapons against the protagonist; Julius asks if the protagonist still has doubts after hearing the sins of the others.
-In the Hero's story, the Hero tell the Heroine that since they encountered again in Cascade Cottage, despite putting up the facade of the tough guy, he longed to be protected by the Heroine, remarking how he has never matured unlike her.
-In the Heroine's story, she tells him that since they meet at Cascade Cottage, she recognizes that all of his actions reflect his pure heart compared to her who only runs away and makes excuses, which makes him a better person than she is.
Then in both stories, the protagonists casts aside the rusty Mana Sword as a symbolic act. Julius' shadow asks the protagonist if they've thrown away the fate of the world, but the hero responds that they have thrown away all their doubts at last; unlike him who has cast aside his heart and that he could never understand such an action.
The protagonist refuses to fight their counterpart, even as the shadow took control of them, and thanks them for everything; the protagonist readies to receive the gracing blow, but their counterpart misses and breaks away from the shadow's spell. Suddenly, the other main character responds by asking everyone for strength, so in in various parts of the world, it's shown Count Lee, Isabella and Marley and others giving their strength to them. Therefore, the spell on the other aliies is broken, and then Cibba arrives.
Bogard reveals that his wife was the Heroine's mother, making him the Heroine's father; the Heroine says she somehow already knew this, and despite it, he would always be her Sir Bogard within her heart. The Hero, in turn, is left perplexed.
Lester tells the shadow that there are no weaknesses without strength, as Willy also says that despite the occasional doubts they still accept each other, leaving the shadow annoyed, calling them lower life forms; Cibba tells him that it is he who has yet to evolve, just like the old times. Angry, the shadow then calls for his master, who soon answers. in plead of more power.
A person is teleported into the room, which the Hero identifies as Lord Granz. The shadow laughs at Granz's fate, revealing that all shadows and monsters have taken a share of his life force to become stronger, and that the heroes have unwittingly weakened him as they journeyed through their adventure. Once again the shadow tries to demoralize them.
Bogard tells the protagonists to continue without them, which the others agree. The shadow mocks their idea of friendship, saying they're not that different from Julius, and then knocks them with his magic. The shadow tries manipulating the protagonists, convicing them to use their friends as stepping stones on their way to become new gods. Suddenly, Granz recovers and breaks from Julius' spell, sending forth a beam of light to the shadow to weaken it. Granz entrusts the future to the protagonists and sends them to the Mana Tree. The Hero and Heroine are transported, while their allies remain to take care of the shadows of Julius.
So, after an encouraging speech to keep fighting, the two progress forward to confront Julius. Julius tells them it's already late and that he has claimed the Mana power of the Mana tree, leaving it to wither. The villain reveals that he only wanted to attain unlimited power to become to ruler of the world to meet the Mana Goddess, claiming that in such a way, she would become an ordinary woman. While not sure why, he seems to want her to become his woman.
Julius offers the Heroine to come with him to free her from her fate: the fate of becoming the next Mana Tree. Julius says that there really is no Mana Goddess, that only humans exist in the world. Just as Bogard brought his wife, Mana, as sacrifice to the Sanctuary, the Hero repeated these actions, making him wonder of the futility of his actions. Julius tells the heroes to join him to become free of their fates, but the Hero does not waver and his resolve and the wishes of everyone makes the Sword of Mana shine again. The heroes ready to face Julius at last...
After the battle, the villain mocks their victory, saying their strength is not of them but of the Sword; but the Hero tells him that its true strength comes from the heart of its wielder. The Heroine tells him to stop his madness; that without Mana the world would cease to exist; but Julius' implies that the point of his quest was just to usher a new age without Mana power, perhaps to make mankind move forward. Annoyed, Julius amasses Mana. The heroes ready for the final battle, as the Mana surge sends them towards the Limbo.
After a long battle, Julius is finally defeated, but as he vanishes, he tells the heroes that as long as Mana remains he will return...
The heroes and their allies celebrate their victory and vow to rebuild the world, while Cibba tells them that it should be time to leave the protection of the Mana Tree. The Hero tells the Heroine that no matter her form, he will always be there to protect her, and so the Heroine waves goodbye to everyone and becomes the successor of the Mana Tree. Time eventually passes and the Hero returns once again to the Mana Temple, to the new Mana Tree, and leaves the Sword of Mana on its roots, perhaps to remark his vow.
Spoiler ends here.
