The Ship’s 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 after the Second Host in the area that would come to be known as the Ho-Lo Shan Mountains of Northern Mongolia, to monitor humanity's progress.
Around Circa 1100 A.D., a Mongolian immortal and External, known as Garbha-Hsien (and later known as Saul), discovered the Ship and lived next to it while he researched its mysteries. Garbha-Hsien never attempted to enter the Ship.
Fifty years later, the Egyptian immortal, En Sabah Nur, learned of Garbha-Hsien and sought him out as another immortal. In a confrontation, En Sabah Nur slew all of Garbha-Hsien's guards. Garbha-Hsien then sought to humble his fellow "forever-walker" by revealing the secret titanic vessel. Having had previous experience with futuristic technology, Nur attacked Garbha-Hsien and left the other immortal for dead. Garbha-Hsien survived, but fled.
Nur entered the Ship and emerged later as a vastly changed being. Nur lived on the Ship for many years not fully understanding how to communicate with it or control it. Nur was introduced with a solution from a young man, calling himself the Traveler. In a battle between Nur and Traveler, Nur severed Traveler's left cybernetic arm and, during the confusion, the Traveler pulled a gun and shot him in the head. Ozymandias, Nur's servant, had Nur's body returned to Ship. With the Traveler's blood mixed with the Techno-Organic Virus and his own, Nur was healed in a chamber of Ship and, infected with the virus, could then understand Ship. After understanding what he had done, Traveler sent both Ship and its passengers far into space.
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 Nur's, cloaked mobile headquarters, as he called himself Apocalypse and attacked New York with his Four Horsemen. After the defeat of Apocalypse, Ship crash landed on X-Factor's Complex. During the battle, the Ship's cloaking and navigation systems were damaged. 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.
While sleeping, X-Factor and their students were attacked by Ship, still under the control of Apocalypse, until Rusty Collins freed its consciousness and X-Factor expelled a bomb and Ship, now able to speak, asked to join them. 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. Realizing that his presence was unsettling for the citizens of Manhattan, Ship moved X-Factor over the Atlantic Ocean.[5] While playing around on Ship, the students ran into Beast, who was going over old photos of X-Factor in their teens and revealed their origins, as the original X-Men and students at the Xavier's School for Gifted Youngsters.
After Iceman was tricked by Infectia to allow her on Ship, Beast attempted to warn Iceman, who was being seduced by her, but due to Beast's lack of intelligence, Iceman couldn't understand him and the students and Ship kept her from kissing Iceman. After Infectia retired to her quarters, she threatened to alter Ship on a molecular level if it continued to obstruct her plans and Ship, fearing the same enslavement Apocalypse inflicted, asked Beast to intervene.
After the Xartans and Lord Zano, in Avengers disguise, attacked X-Factor, the children were protected by Ship, who was attempting to atone for endangering Iceman, but later allowed the children to aid X-Factor. After saving Iceman from her kiss, however, the powers of the Infectia's kiss, on Beast, reverted Dr. Maddicks' and Pestilence's change and triggered the Beast's return to his intelligent, blue, furry, more animalistic look, but much stronger, while Ship was caring for his recovery. After Beast was restored to health, Ship teleported him and Cyclops to aid X-Factor and the students against the Alliance of Evil.
After the Inferno of Manhattan, the students of X-Factor began calling themselves the X-Terminators and were partnered with the New Mutants. The two young mutant teams returned to Ship with thirteen mutant babies and Ship individually scanned each of them, for mutants. The aliens, Warlock and Gosamyr set Ship's danger sensors off. Although Ship was convinced to allow Warlock to stay, he refused to allow Gosamyr, stating that she should not be allowed to live, and crafted a ship to send her off planet. Also, Cyclops' son, Nathan Summers, and Marvel Girl's parents were left on Ship (Marvel Girl's parents were literally left "on" Ship, due to the fact that he could not allow humans inside), while X-Factor and the X-Men battled Mr. Sinister and the Marauders. Due to their actions during the demonic invasion, the X-Terminators were expelled from Phillips Academy and, while the New Mutants returned home and X-Factor attended funerals, the X-Terminators found an Atlantean horn and accidentally called a giant sea creature that attacked Ship. The New Mutants returned and, with the aid of Namor the Submariner, they defeated it. After the creature's defeat, X-Factor returned and the New Mutants began to live on Ship, as Professor X's mansion had been destroyed. While X-Factor was on a mission in London, the New Mutants had Ship diagnose Mirage and her horse, Brightwind, and Ship learned that they were infected with a mystical illness. Ship suggested the New Mutants go to Dr. Strange for assistance.
After being recalled across space by Gammenon the Gatherer, Ship took to space, with X-Factor unwittingly along for the ride. After Gammenon sensed their presence, X-Factor was sent to the alien planet below, where they were split-up during a battle between the Chosen and Rejects. While being held in the hand of Gammenon, Ship remembered his prime directive and recited all of his data knowledge, after Apocalypse enslaved his conscience. Gammenon did not release Ship and Ship realized that he did not correctly recite all of his knowledge, which forced Ship to remember his past before Apocalypse's enslavement. The Celestials collected the data Ship had gathered during its stay on Earth and Ship came to realize that Apocalypse hadn't created it. Noticing that the Celestials were heading towards the planet below to destroy it, Ship broke free of the tractor beam and descended to rescue the planet and his friends. 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.
Apocalypse later sent his Riders of the Storm to kidnap the infant Nathan, from within Ship.The Riders of the Storm infected Ship with the Techno-Organic Virus, that damaged its systems and caused Ship to attack New York. 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, with the Inhumans.[20] After Nathan was rescued, X-Factor found that baby Nathan had also been infected with the T-O virus and that it threatened his life. Ship created a protective electromagnetic field and merged with Nathan's electrical parts, to keep the child alive. As the virus spread through Nathan's body, threatening to turn Nathan into a body of liquid metal and organic steel, a member of the Askani Cult, Sister Askani, who sacrificed her physical body to become energy, appeared from the late 37th-early 39th century to Cyclops, claiming that Nathan would become a savior in their time and that the Clan would cure him of the virus. Choosing to save his son's life, believing that he would never see him again, Cyclops agreed and Nathan was taken into an alternate future ruled by Apocalypse. 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 traveled on his own and was captured, by 'Strator Umbridge, and met Blaquesmith. While Nathan was imprisoned, his Techno-Organic Virus infection worsened and Blaquesmith, a member of Clan Askani, broke into his cell and extracted a glowing orb from the metallic flesh of Nathan's chest. The orb was Ship's A.I., which, forgetting its past, had begun to call itself "Professor". Nathan then kept the Professor as an ally, who spoke and could control electronic devices. At one time, Stryfe, Nathan's evil clone, captured Tetherblood, one of Nathan's soldiers, and the Professor from Nathan's camp and Stryfe tortured Tetherblood to find out its importance. The withdraw of the Professor from Nathan caused him to become very sick and Blaquesmith sent Aliya, another Clan member, to the past to find Cable, the adult Nathan. Aliya was successful, though unaware of Cable's true origin. Cable returned with the flask and activated Ship's A.I., which again merged with Nathan. Professor lived within Nathan's techno-organic flesh, acting as adviser to him and helping to control the T-O infection.
