Yuan doesn't have any hatred built up towards Kratos, he just realizes he needs to be taken down in order to accomplish his own goals, especially because Kratos is still apart of Cruxis with Mithos. Yuan tells Lloyd that Kratos is a deceiver, and his heart has been long dead. He tells them to go save Colette as he screams out to Kratos, "Look at me! The true fight starts now!" The two battle, allowing Lloyd to take Colette back. The next time they are all together, Yuan screams out to Kratos to release Origin other wise his son, Lloyd, will die. Lloyd is shocked and can't believe what he heard, because Yuan spoils the news that Kratos is his father. Yuan realizes that he can use their family relation to get Kratos to release his pact with Origin, although it could ultimately kill him. Without Origin, Cruxis won't have a hold on the Eternal Sword, allowing them to have an upper advantage.

At this point in their relationship, Yuan does not want Kratos to die, but he needs to play both him and Lloyd in order to get Origin released so that Sheena can make a new pact with him. Yuan is no longer thinking about his former friends, he is just concerned about righting the wrongs he already committed.

The two end up getting in a devastating battle, both using their ultimate attacks on each other. They both end up badly injured and lay on the ground silent for awhile. Yuan asks Kratos why it had to come to this? Kratos admits that they were all wrong, all wrong in what they had become with Mithos. Yuan and Kratos wonder whether or not their wrongs could be undone, or if it is simply too late. Yuan tries to have a glimpse of hope for both of them, and asks him if he wants to go find out if their is hope in his son, Lloyd, to fix the mistakes they made and create the better future that Martel would have wanted. The two go and tell Lloyd and the gang all about the mistakes they made, and give them the encouragement to go and save the world. However, Kratos and Yuan know that Kratos must release Origin, even though that may mean death for Kratos. Yuan is more concerned about this in the OVA than in the game, however. He comes up with an idea, that after Kratos releases his mana to release Origin, he will give Kratos some of his own mana in hopes that Kratos can live. Kratos starts to protest, stating that Yuan may die as well. Yuan says he can't give all of the spotlight to Kratos, and besides they've both lived long enough. Kratos grins and calls Yuan twist. The two get in a sort of playful fight, where Yuan tells him he didn't always like him. But the time comes, and Kratos begins to release Origin. Yuan looks disturbed and sad as Kratos loses his mana. Kratos collapses, and Yuan catches him in his arms. Blood running down his face, Kratos looks up at Yuan as Yuan gives off his mana back into Kratos. Yuan asks him if he's okay, and Kratos smiles at him. The two grin and look off into the distance, knowing that they can't take back what they have done, but they are on the journey to changing the world for the better now, together! For what Martel truly wanted. As the two walk back towards where the action was going down, a ray of light shot up into the sky. They both new that Mithos had died. They look sad to the ground, and Yuan states, "We lost hope for the future when Martel died. Neither of us tried to stop him. We took too long to notice." They mourned the loss of their dear friend who neither of them stopped in time, and continue to walk towards Lloyd and the others to see the new world together.

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