In What If? (2nd series) #minus 1, Fitzroy's escape from the Pool took him further back in time than his trip in the main timeline. He arrived several years prior to the formation of the X-Men. Fitzroy saw an opportunity to prevent the X-Men, and therefore the X.S.E., from having ever been formed. Trevor presented himself to a younger, more naive Charles Xavier with a message from the 
future. By using half-truths and allowing Xavier to telepathically pull select images from his mind out of context, Fitzroy convinced Xavier his dream to gather together young mutants would lead to the formation of a brutally aggressive and fascist X.S.E. in his time period. Adding to Fitzroy's ruse, Bishop had followed him back in time and was wanted by the police for a murder Trevor had committed. Xavier had not yet come around to the idea of an outlaw team of mutants, and instinctively doubted Bishop simply because the authorities did. When they met, Bishop's hatred for Fitzroy and tendency towards violence only convinced Xavier of Fitzroy's honeyed words. Xavier turned Bishop over to the government as a murderer, and the X-Men were apparently never formed.
In What If? (2nd series) #84, Fitzroy made a daring raid on X.S.E. headquarters and ended up in a stand-off with Bishop and Shard. Fitzroy held Bishop at gunpoint and ultimately killed him before Shard could stop him. Therefore, when Fitzroy fled back into the past, it was Shard who pursued him. Shard was driven by vengeance and lacked the hero worship of the X-Men that defined Bishop's character. She thus had no qualms about using the X-Men as allies to get close to Fitzroy and murder him for killing her brother, despite the X-Men's objections to her methods.