Following his adventures, Terra decides to visit the Mysterious Tower to seek advice from Eraqus's fellow master Yen Sid. After catching a glimpse of Yen Sid's apprentice Mickey Mouse, Terra talks to Yen Sid about Xehanort's disappearance, the Unversed, and the masked boy. Yen Sid simply tells Terra to treat all three as the same problem.
Leaving the tower, Terra is contacted by Master Xehanort, who tells him to meet at the Badlands. There, Xehanort explains that the masked boy, the master of the Unversed, is his rogue apprentice and creation Vanitas. As Xehanort claims, Ventus used to be Xehanort's apprentice, but when Ven had succumbed to darkness, Xehanort ripped the darkness from him and accidentally created Vanitas. Xehanort explains that Vanitas is headed to Radiant Garden, the city of light, and tells Terra to go there and bring him down.
Arriving at Radiant Garden, Terra catches Xehanort waking in the streets, and pursues him, briefly stumbling upon the wizard Merlin and a book that Terra can read to unlock hidden powers. As he leaves, an Unversed passes by, and Terra chases it to the world's Reactor. Much to Terra's surprise, Ven and Aqua are also there, having pursued other Unversed to the same area. The three Unversed merge to the Trinity Armor, and the three Keyblade wielders defeat the armor. Despite this, arguments abound; Terra is concerned upon learning that Ven had encountered Vanitas, forcing Ven to separate, while Aqua is accused of following Terra around for his own good. Upset, Terra leaves.
At the lower portions of the castle, Terra meets Braig, a mercenary who claims to have abducted Master Xehanort. Terra follows Braig to the Outer Gardens and finds Xehanort imprisoned. Braig explains that he kidnapped Xehanort in order to learn how to wield a Keyblade for himself. As the two fight, Terra struggles against Braig, but Xehanort orders Terra to fight for Master Eraqus. Eventually, the fight ends with Terra using the darkness to scar Braig's face, forcing him to flee. With Xehanort free, he takes in Terra as his pupil, striking an alliance to bring an end to Vanitas. Terra soon leaves Radiant Garden to find Vanitas, even after Ven wants to come too.
Back in the Outer Gardens, it turns out that Xehanort and Braig had been faking the abduction this whole time, with a bandaged Braig attempting to gun down Xehanort for letting him become collateral damage. However, Xehanort reminds Braig that there is more to do...