After Hal's expulsion and Kyle's departure, John Stewart joined Guy Gardner and others in investigating recent attacks in a distant sector of space, which were revealed to be the result of an old Guardian experiment. At one point, John was forced to kill another Lantern who was about to give in to torture and reveal the access codes to the Oan defence network. John was approached by the Alpha Lantern to arrest him for the murder of Green Lantern member. He was found guilty for this crime and sentenced to death. However Guy Gardner and other fellow lanterns freed him before the execution, resulting in the destruction of the Alpha Lanterns when the Green Lanterns refused to allow John to be executed. During the fights, the Alpha Lanterns (revealing to the reader that the Guardians set up these events as part of their plans to destroy the Corps) realized that all the Alpha Lanterns had become dangerously mentally unstable. Alpha Lantern Varix caused a reaction which killed all the Alpha Lanterns, including himself.
John was contacted by the Guardians who stated that Mogo's remains appeared to be moving and that they had come to the conclusion that Mogo was trying to reform, and assigned him to track it. While tracking the Mogo fragment's destination, he was discovered by Fatality, who was seeking a sundered love in danger. After they found Mogo's pieces, John had figured out about the Guardians wanting to use Mogo. After the villainous First Lantern was destroyed and the unemotional Guardians were killed off by Sinestro, John began a relationship with Fatality on Mogo.