Soon, the group finally heads to the Tower of Salvation and Colette readies herself to become one with the Goddess Martel. However, the oracle reveals that Colette will lose herself completely in the process and will merely become a vessel for the goddess, in other words, dying in spirit. Lloyd, hysterical over losing Colette tries to talk her out of it, but she convinces him to let her go and eventually sacrifices herself for the cause. The oracle, Remiel, then reveals that he had ulterior motives with Colette all along, meaning that the Church of Martel may not be all that it seems. He attempts to kill the remaining party members, but is defeated and summarily killed by Kratos. However, this is not a joyous event, as Kratos then reveals himself to actually be a high-ranking member of the same organization as Remiel belonged, Cruxis. A battle for Colette then results, but ends with yet another figure entering the scene: Yggdrasil, an angel who reveals himself to led both the Desians and Cruxis. He then attempts to kill the party on his own, but they are saved by a mysterious group of people at the last possible moment and are whisked away to a separate location.
The group wakes and finds themselves in the main base of the Renegades, a covert resistance group of half-elves and humans that fight against Cruxis. Coincidentally, they bear a strong resemblance to the Desians and were the ones originally responsible for the first attempt on Colette's life. Their leader, Yuan, explains that this is because they wished to stop the World Regeneration process because it is actually hurting the planet. Even more shockingly, he reveals to the group that there are in fact two worlds, the current world they reside in and Tethe'alla, a world that lies on a shifted dimension to Sylvarant which they cannot actually see, but are connected to and affect with actions in regards to the mana supply. He further explains that the World Regeneration process is actually a reversal of the flow of mana from one world to another. The balance of the two worlds in much like an hourglass: one world is flourishing and the other is in decline. Sylvarant, due to their failures in the World Regeneration, is in decline at present, but Colette releasing the seals has begun the process of reversing the flow of mana back to Sylvarant. However, due to the fact that Colette has completed her transformation into an angelic being, she is now useless as a pawn for the Renegades, as she will kill anyone who attempts to come near her. But the group then finds themselves double-crossed, as Yuan attempts to capture Lloyd for unknown reasons. They fight their way to freedom and actually manage to make their way to Tethe'alla via special vehicles called Rheairds, though they end up crashing into a mountain range as a result of Tethe'alla beginning its approach to decline (as the vehicles run on a specific form of mana which is no longer available).
Lloyd, Colette, Genis and their teacher, Raine, along with another companion, Sheena, then make their way to the Imperial City of Meltokio in order to ask for assistance with transforming Colette back to her normal self (Sheena, being from Tethe'alla, informed them that her world has a Chosen as well and are currently researching the Cruxis Crystal he was also given). They go through many trials and tribulations upon their arrival, including but not limited to sneaking into the castle, knocking out several guards and almost being killed from being from Sylvarant once they finally manage to meet the king. However, they manage to convince the Pope to allow them to find a cure for Colette, but only while under the supervision of Tethe'alla's Chosen, Zelos.
Finally, the group begins their extremely perilous journey across Tethe'alla, coming in direct contact with the deeply embedded caste system in the world, which declares that all half-elves that commit a crime are to be executed. This results in a rescue effort to save Raine and Genis, who are revealed to be half-elves. Yet more issues arrive after a cure is found for Colette, stemming from the Desians, who have also apparently come into Tethe'alla, and the revealed knowledge that the Renegade leader, Yuan, is actually also part of Cruxis. Ultimately, the group decides that even though Colette is cured, they will search for a way to reunite the two worlds, even if it means taking on Yggdrasil again. However, this process involves them dealing with the forces of nature itself, as they must forge pacts with the eight Summon Spirits of both worlds (who are in charge of balancing the mana) in order to reunite them. But more misfortune befalls them, as Colette is kidnapped and comes down with an even deadlier illness after her rescue, not to mention that several entities from Cruxis and the Church of Martel have begun chasing them all over Tethe'alla.
They are finally able to reach their goal of making pacts with the Spirits of both worlds, which accomplished the separation of the two worlds through the mana links. However, a new obstacle is introduced into the fray. The Great Seed, called in legend the Soul of Mithos, is actually the last remaining seed of the Great Kharlan Tree from the ancient war. As a result of the mana links being severed, the Great Tree starts to grow wildly out of control, growing into a grotesque form visible from both worlds. The tree, in its unstable state from over-absorbing Sylvarant's mana, now threatens to destroy both worlds. Lloyd and his friends manage to avert this by firing mana from the opposing Summon Spirits at the tree, but the Tower of Salvation, the pinnacle of hope that signals the coming of the World Regeneration, is destroyed in the process in Sylvarant.
