The Ship A.I. was created untold millennia ago by the Celestials as the operating system for a data collection device. The Celestials had genetically manipulated humanity, and they left the Ship in the area that would come to be known as Mongolia to monitor humanity's progress.
Circa 1100 A.D., a Mongolian immortal known as Garbha-Hsien (later known as Saul), discovered the Ship and lived next to it while he researched its mysteries. Saul never attempted to enter the Ship.
In time, the Egyptian immortal En Sabah Nur learned of Saul and sought him out as another immortal. In a confrontation, En Sabah Nur slew all of Saul's guards. Saul then sought to humble his fellow 'forever-walker' by revealing the secret titanic vessel. Having had previous experience with futuristic technology, Nur attacked Saul and left the other immortal for dead and entered the Ship. He emerged later as a vastly changed being who now called himself Apocalypse.
Over the next few centuries, Ship's sentience slowly evolved. Apocalypse noticed the evolving A.I. and enslaved it, telling Ship that he had created it.
The Ship next appeared as Apocalypse's cloaked mobile headquarters as he attacked New York with his Four Horsemen. Defeated by X-Factor, Apocalypse retreated, and was forced to leave the Ship behind. During the battle, the Ship's cloaking and navigation systems were damaged. X-Factor managed to get the Ship to safely crash in the river. The only building damaged in the crash was X-Factor's own headquarters. Conveniently, the Ship also projected a force field that prevented non-mutants from entering. Given these reasons, X-Factor decided to adopt the Ship as their new home base.
When X-Factor tried to move in, they discovered that the Ship was booby-trapped, but then the Ship A.I. revealed itself and assisted them, and Rusty Collins, in disabling the security. Ship then became a butler of sorts to the team. Ship "had complete control over every part of its structure and could fashion rooms, weapons and vehicles as needed from various storehouses and parts it had. It was able to design and run training programs for X-Factor, as well as make living quarters and workshop areas for them."
In time, Ship took to space, responding to the call of the Celestials, with X-Factor unwittingly along for the ride. The Celestials collected the data Ship had gathered during its stay on Earth and Ship came to realize that Apocalypse hadn't created it. The Celestials showed it its true origin. Given the choice, the Ship A.I. decided to return to Earth with X-Factor. Upon return from the space journey, Ship landed on-end as a building in Lower Manhattan.
An attempt by the mutant called Infectia to steal the craft led to X-Factor ultimately moving Ship to a more mobile position over the Atlantic Ocean.
Ship played host to the New Mutants and the X-terminators for some time, as Professor X's mansion had been destroyed. Unfortunately this did not stop him attacking them when they brought on board the entity known as Gosamyr. The two sides fought to a standstill, until Ship was persuaded to generate a spacecraft that would take Gosamyr away from Earth.
Apocalypse later sent his Dark Riders to kidnap the infant Nathan Christopher Summers from within Ship. The Dark Riders infected Ship with a techno-organic virus that damaged its systems. Explosion imminent, Ship launched itself into space to protect the city.
The Ship A.I. managed to salvage itself as an energy construct which was able to protect and ferry X-Factor to the Blue Area of the Moon, where they joined the massive confrontation against Apocalypse. X-Factor found that baby Nathan had also been infected with the T-O virus, and that it threatened his life. A mysterious stranger named Askani appeared and offered to take Nathan to the future, where technology would be capable of saving him. As Ship's energy form lost cohesiveness, it spent the remainder of its energy protecting Nathan Christopher on the trip. Although Ship's energy was dissipated in this way, when Nathan arrived in the future, there was no trace or mention of Ship.
After arriving in the future, Nathan's T-O virus went into remission. Around 16 years after arriving in the future, Nathan was imprisoned, and his techno-organic virus infection worsened. Blaquesmith broke into the prison and extracted a glowing orb from the metallic flesh of Nathan's chest. The orb was the Ship A.I., which, forgetting its past, had begun to call itself "Professor." Professor lived within Nathan's techno-organic flesh, acting as adviser to Nathan and helping to control the T-O infection. In time, Nathan became known as Cable.
Deciding to change his tactics for bettering the future, Cable returned to times close to the present day. He shuttled between past and future multiple times, at one point bringing with him his space station Graymalkin. Professor had assumed control of Graymalkin, performing duties similar to those it had as Ship. Graymalkin not only served as a base for Cable, but also allowed Cable to teleport through time and space.
Eventually, Graymalkin was destroyed in a battle between X-Force against War Machine and agents of S.H.I.E.L.D., although parts of the station were jettisoned safely to Earth. Magneto later salvaged the wreckage in space, combining it with that of his old Asteroid M base to form his new space-borne home Avalon. Cable undertook a raid on the station and, despite suffering heavy damage he was able to download Professor back into his own techno-organics.
Cable installed Professor in X-Force's Camp Verde, AZ bunker base. During the Phalanx Covenant storyline, the Phalanx attempted to assimilate the camp's systems but were overwhelmed by the Professor's Celestial and future technology. X-Force returned to find that the Ship A.I. had gained a T-O body and was now calling itself Prosh.
X-Force learned that Prosh's techno-organics were interfering with Cable's control over his own infection. Having come out of remission, the infection was killing Cable. Despite having befriended the X-Force team, Prosh had to leave. With Warpath's permission, it assimilated the remainder of the base with the exception of the burial grounds. With the greater bulk, Prosh formed a spaceship again and flew off into space.
Prosh later returned as a key figure in the X-Men Forever mini-series, but that miniseries has debatable canonicity per Marvel's editorial decisions.