After hearing that Chocolat, together with some other people, was captured by the Desians, Lloyd Irving and the others go to the ranch to free them. However, they are stopped by Neil, who wants to warn them. Kratos Aurion and Raine Sage figure that he wants to tell them that Dorr is trying to trap Colette Brunel, because he is working with the Desians. Although they all are shocked by it, Neil says that it is right. He wants them to continue the Journey of Regeneration and let him fix things out. However, Lloyd refuses to do that, and they decide to infiltrate the ranch. Depending on Lloyd's choice, they may or may not infiltrate the ranch before confronting Dorr in Palmacosta. If they decide to confront Dorr first, they will get a card that opens one of the doors, while they will have to get inside another way without.
When inside, the party will have to look after three colored cards, and also use the Sorcerer's Ring's next challenge. On their way, Lloyd and the others manage to release the prisoners, and Neil tells them that he will lead them out to safety, so they shall just go and find Chocolat, who is not found anywhere. When they eventually get to Chocolat, they have to fight against some highly-ranked Desians. When they are defeated, Chocolat thanks them for saving her, and asks if Dorr is coming, as well. Not wanting to tell her the truth, they lie and answer positively. She shows them the way to Mangius' office, but when they get there, they are surrendered. Magnius then introduces them to a form of magitechnology. It shows Neil and the other prisoners on their way out, but are stopped when all the doors are closed, and they are trapped in a room.
Magnius laughs at the group's shocked expressions, and asks Lloyd if he wants them to turn into monster by losing their Exspheres, just like Marble. Chocolat is astonished by hearing the name, and Magnius reveals that Marble was Chocolat's grandmother, who was taken to his ranch. However, she was transferred to Iselia Human Ranch, where, according to Magnius, Lloyd killed her in a painfully way. Genis Sage tries to explain to Chocolat that it is not the case; that Lloyd actually tried to save Marble. However, Chocolat does not believe him, and backs away as she gets captured by Desians and taken away. Lloyd tries to stop them, but Chocolat rejects him, refusing to be saved by her grandmother's murder. Colette tries to calm her down, but Chocolat refuses, and is eventually taken away. They try to follow her, but are stopped by more Desians, who they fight and defeat.
Magnius, furious that his subrogates lost, gets up and challenges the group instead. However, when he is defeated, he is surprised when Kratos tell him that Cruxis has accepted Colette as the Chosen of Mana and says that he was deceived. Then he passes out. Raine tells them that she has activated the self-destruction system, so they have to get away. They leave Magnius behind, but Mangius manages to wake up and mumbles that he must warn Forcystus before it is too late. However, a man he names Rodyle comes forth in the projector, and tells Magnius that he will not be able to get contact with the fellow Grand Cardinal. Magnius curses Rodyle, revealing that the latter told him that Magnius had been ordered to kill the Chosen. When Rodyle's image vanishes, Magnius uses his last minutes to bless Yggdrasill's age of half-elves. The human ranch is then destroyed.
When the group travels to the Palmacosta Human Ranch because there has been rumors of movements there, they meet up with the Renegades, which was mistaken to be Desians. Yuan Ka-Fai appears and asks them what they know about the Kharlan Tree. Zelos explains that it is the tree of mana that can produce countless amount of mana. Genis, however, says that it is just a fairy tale, though Yuan says that it does exist, hidden. They agree to work together, and Yuan leaves for the preparations. Botta is there to wait for the group to get ready.