Thanks to the work of Lloyd and his companions, a new Tree was planted to replace the Giant Kharlan Tree, reuniting the two world back together. This was the story of the Journey of Regeneration.

Even with the world united, people are still facing numerous problems. Due to the merging of the worlds, maps have become useless & the climate in various areas has encountered vast changes: desert towns have frozen over, and lakes have dried up unto vallies. All of this stems from a single factor that was overlooked: the spirit of the old Giant Kharlan Tree, Ratatosk, exists somewhere in the world, in a deep slumber. That slumber has sent the united world into chaos.

There is another problem, however. Tensions have been escalating between the citizens of both worlds. The citizens of Tethe'alla look down upon the citizens of Sylvarant, due to their inferior technology. On the flip side, the citizens of Sylvarant fear the citizens of Tethe'alla due to their technology. Two years have passed since the merging of the two worlds, and the citizens of Sylvarant have banded together to form the "Vanguard", which aims to rise against the Church of Martel (and inherently, the citizens of Tethe'alla).

One day, the Church of Martel launches an attack against the Vanguard. Palmacosta, one of Sylvarant's cities, is caught in the crossfire. Numerous innocents are killed, and the city is consumed in flames. This day came to be known as the "Bloody Purge", which allegedly was led by Lloyd Irving (working for the Church of Martel).