Returning to Tethe'alla our heroes head toward Origin's resting place. Kratos is waiting for him there. Lloyd doesn't want to fight him, but Kratos says he must. He does fight, and wins, but Yuan appears and saves Kratos before he dies completely. They release Origin and receive the eternal sword. But Lloyd can't use it because he has no elvish blood.
The others go back to Sylvarant where they prepare for the final battle. Lloyd is given a sword by each of his fathers. They become the eternal sword and he is somehow able to use it. They head off to face Mithos Yggdrasil in a final showdown. He is defeated and the eternal sword recombines into one (it had split into two and entered Lloyd's swords from his fathers) and offers to grant Lloyd a wish. He wishes for the worlds to be reunited and saved, no longer sharing mana. The sword complies and the mana tree grows normally once more. Kratos takes the Desians and goes back to Derris Kharlan (a third world that was held very close to the other two by the power of the eternal sword) determined to leave and never come back - rather sad considering that he and Lloyd just got to the point where they really were almost like a real father and son. At least Lloyd and Colette are going to stay together, and it's looking like their relationship has finally become more romantic over the course of the journey. Everyone else has faced their inner demons and are much more confident, stable people. Plus, there is a new summon spirit - the Spirit of Rebirth. And with her watching over everything we'll trust that the newly reunited people of the two worlds won't fall back into the war that caused Mithos to separate them in the first place...
Now was that confusing or what? Anyway, I'm going to put up the detailed summaries from the game synopsis, but be warned! They aren't in chronological order, I don't know why they game puts them in such a strange order, but it does... I tried to rearrange some of them, but it's been so long since I've played that it was really hard. I was doing it based on the level we were at when we finished it. But even then it was sometimes hard. Anyway, it's just basically going to be if you wanted to know where a specific problem was resolved or something.