Do you mean Ship from the X-factor comics? As I recall, it was actually made by the Celestials, and Apocalypse later showed up in it. X-factor (if I recall the arc) took it over, reprogrammed the Ship AI (that was the only name I remember them ever giving) and then it landed and became, for a time, a building. They were still in residence when the whole Dark Riders/kidnapping of Nathan/Techno-organic virus/Askani thing happened...
WAIT! Didn't the Ship AI start calling itself "Professor" or something in the future, and live inside nathan's/Cable's body, acting sort of like a Merlin to his Arthur? I remember i kinds likeds that arc, if I'm recalling it properly.