Lloyd ends up being seen (protecting Genis by creating a distraction) and the Desians attack Iselia in retaliation. He and Genis are exiled by the townspeople. They set off with Colette to save the world. This begins with travels to the various temples. But there are complications because Lloyd is wanted by the Desians and by another group we discover is called the Renegades. These are the people who attacked Colette at the first temple. They are evidently trying to foil the Desian's plans. Then there's the strange, clumsy, assassin who is trying to kill Colette. As Colette opens seals she becomes less and less human. They also befriend the would-be assassin. Her name is Sheena and she claims to be from another world that shares Mana with Sylvarant. If Colette succeeds in reversing the flow of Mana, her world will fall into decline. Now she doesn't know what to do. Finally they reach the Tower of Salvation and the truth is revealed. The actual purpose of the chosen is to be taken and used as a vessel for the spirit of Martel, the sister of Yggdrasil, leader of the Desians. He made up the goddess story, and the whole religion, to bring his sister back to life. Even worse, Kratos actually works for Yggsrasil, he is one of the Four Seraphim - leaders of Cruxis. Cruxis is in charge of the Desians, but is based in another world. They take Colette, but Lloyd and the others are rescued by the renegades.
They escape the renegades, but end up in Sheena's world, Tethe'alla. They do manage to save Colette, but she is an empty shell thanks to the exsphere at her throat. Lloyd makes her a keycrest which returns her to normal. They decide that they have to find a way to save both worlds, but that isn't easy. They discover that the renegades are actually working with the Desians under Cruxis, but the leader of the Renegades is secretly plotting against Yggdrasil. His name is Yuan, and he convinces Lloyd to trust him. Plus, Kratos keeps popping up and giving Lloyd advice. They pick up three new friends, one of whom originally tried to capture them, and a whole lot of new enemies and problems. Plus Colette has been hiding something from them - she's sick, and they don't know how to help her. Raine and Genis turn out to be half-elves, when all along Raine had told everyone they were full. And they are from Tethe'alla! Plus, the people of Tethe'alla don't like half-elves.
Yuan convinces them to go make pacts with all the summon spirits, effectively shutting off the mana supply entirely. He thinks it will allow them to resurrect the great tree and save the worlds, but it does the opposite. When they try to fix it the great tree goes crazy and destroys half of Sylvarant. They use the summon spirits of Tethe'alla to stop it.
They set out for answers on how to save Colette and both worlds. They do manage to heal Colette, but Yggdrasil is still after here. They discover another world very near theirs that is filled with lifeless 'angels' and can only be reached through the Tower of Salvation (which is the only thing that exists in both Sylvarant and Tethe'alla). They befriend a young half-elf named Mithos and then discover that Yggdrasil used is actually Mithos Yggdrasil, hero of the Kharlan war. And he is also Mithos the boy they have befriended. Mithos once saved the worlds from war by separating them into two worlds. But he became obsessed with bringing his sister back from the dead and has become a fallen hero. Kratos is loyal to him only because Kratos was once his mentor and feels somewhat responsible. Yuan was also a friend of Kratos and Mithos, traveling with them, but he has decided that he can no longer support Mithos. We also discover that Kratos is Lloyd's father.
They find that the only way to save the worlds is to find the Eternal sword, which was used by Mithos to split the worlds in the first place. They must form a pact with Origin, but to release him Lloyd must release the mana in the one who sealed him. That is Kratos, and the only way to release the Mana is to kill him.
They head to the Tower of Salvation where Zelos, the Chosen of Tethe'alla who had joined them, turns out to be a traitor as well. He allows Colette to be captured. The others go to save her and are caught in an elaborate series of traps. Only Lloyd appears to make it through alive. But Zelos and Kratos then betray Yggdrasil by saving the others and helping Lloyd. They are too late to stop Mithos from transferring his sister's spirit into Colette, but Martel doesn't want to be brought back to life and she gently scolds Mithos and then releases Colette and disappears. Mithos misunderstands and decides he wasn't worthy of his sister's return. He continues with his plan to usher in a new era of lifeless angels.