However, decades after it was taken out of commission, the ship came back online and continued on its original programmed course. Cray, Luke, and Nichos got caught up in the Eye of Palpatine fiasco when Luke probed Nichos' mind for information on Plett's Well, a hiding place for Force-sensitive children on the planet of Belsavis, created by Jedi Master Plett. Nichos was one of the children hidden there, and Luke wished to find the location for any information it might give him on pre-Empire Jedi. The information Luke found led Cray and the group to the Moonflower Nebula where they encountered the Emperor's superweapon. Captured by the ship, the group found themselves prisoners among a number of aliens who were gathered up as well.
Aboard the ship, Cray, Luke, and Nichos found themselves at the mercy of a crazy programmed intelligence, and Cray and Nichos were even sent to a sort of trial and sentenced to die. Eventually, Cray and the Jedi learned that Callista, who had disabled the ship so many years before, had done so by remaining on the ship as a disembodied spirit controlling its actions. Communicating with Callista, Cray and the Jedi formed a plan to destroy the ship once and for all. Part of the plan rested with Nichos and the fact that he had come to terms with his situation. Realizing that no amount of technology would be able to hold his humanity, that it had died with his physical form.
Luke was prepared to sacrifice himself to climb into the core of the ship to blow up the craft, however, Cray stunned Luke and put him on a shuttle off ship, staying behind to complete the job herself. Luke's ship was picked up by Mara Jade, having come searching for him and the Jedi. As the ship exploded, Mara also picked up an escape pod, jettisoned from the ship just before detonation. Inside the pod was Cray's body, but it had changed somehow, with her features noticeably different.
It turned out, that Cray in fact did stay behind on the ship, offering hey body to Jedi Knight Callista so that she might live again. Cray could not bear to live without Nichos, so, she allowed Callista's spirit to enter her body, while Cray's spirit remained behind on the ship as it was destroyed. Together, as lovers, Jedi Knights Cray Mingla and Nichos Marr became one with the Force, while upholding the creed of the Jedi Knights to protect peace throughout the galaxy.