With that last loose end tied up, Gantoris and Luke returned to Yavin IV, where Gantoris was to begin a new life as a Jedi Knight. At the Academy on Yavin IV, Gantoris was one of twelve students Luke had sought out as the first trainees at the Jedi Academy. Gantoris proved to learn quickly and excelled in his studies. He was often at odds, or in competition with Jedi Knight Corran Horn, who was studying at the Academy under the name of Kieran Halcyon for special reasons. During his time at the Academy, when he wasn't studying, Gantoris explored the terrain of Yavin IV with fellow Jedi Knights such as Streen, discovering long lost Massassi Temples. In his private hours however, Gantoris began communicating the spirit of Exar Kun, long dead Dark Lord of the Sith whose spirit had been trapped in the temples on Yavin for over four thousand years.
At first, the spirit of Exar Kun did not reveal his true purposes, but instead helped Gantoris construct a lightsaber, a task Jedi Master Luke had wanted to hold off until he felt his students were ready. During a training session, Gantoris displayed his lightsaber and challenged Luke to a duel. Luke was able to best Gantoris in the duel, but only with a considerable amount of effort. Luke found it disturbing that Gantoris was able to construct a lightsaber, a skill that none of the would-be Jedi should have. Discussing the matter with Gantoris, Luke discovered that Gantoris' visions and nightmares about the 'dark man' were continuing, and Luke admitted that he was beginning to have visions about the 'dark man' as well.
A few nights later, Gantoris was visited by the spirit of Exar Kun in his quarters within the Jedi Academy. This time however, Kun was straightforward about his motives, forcefully trying to get Gantoris to turn to the Dark Side. However, Gantoris resisted Kun's efforts, defying him and denouncing the Dark Side. However, Kun then showed Gantoris an image of his people on Dantooine, being attacked and killed by Admiral Daala's forces, a female Imperial with more futile hopes of uniting the Empire and defeating the Republic. These images were too much for Gantoris to handle, and caused him to lash out at the spirit, but it was a futile effort. Even from beyond the grave, Exar Kun proved to be too powerful for Gantoris and used the Force to burn him to a crisp. Four thousand years after he left his physical form, Exar Kun was able to claim the life of one more Jedi.