Sebastian Shaw remained among the elite in the Age of Apocalypse. His money and mutant abilities kept him protected in Apocalypse’s America, frequently attending the Angel’s night club in Heaven. He still sought to advance his position, however, and acted as an informant to the regime when he saw Worthington conspiring with Gambit, formerly of the X-Men. In the years that followed, Heaven fell and Shaw’s Hellfire Club became a prominent gambling den and brothel for the mutant elite in the former Manhattan. Shaw would play both sides as he fed information to the Red Prophet and the human resistance in exchange for information on his rival, the Minister of Death, Azazel. Shaw would only learn too late that his frequent acquaintance Donald Pierce was also Prophet’s agent, Goodnight. Pierce had Shaw assassinated in his cell after the human resistance finally brought down Weapon Omega and the mutant hierarchy.
In the House of M, Sebastian Shaw apparently worked on the Sentinel project before he discovered he was a mutant. Once he learned the truth, Shaw tried to shut the program down but the technology was already in the works. In the Mutant-Human War, Sebastian supported Magneto and lent his knowledge of Sentinel technology to the mutant efforts, helping sabotage the robots. After the war ended, Sebastian Shaw became Director of the new mutant-led incarnation of S.H.I.E.L.D. under Magneto’s regime. Shaw then commanded the Sentinels for S.H.I.E.L.D., keeping the human population in line. He oversaw various S.H.I.E.L.D. operations, including the elite Red Guard unit led by Wolverine and Mystique. On Battleworld, a reincarnation of this Shaw existed, serving the same role as head of S.H.I.E.L.D. for the House of Magnus.
On Earth-S, the Elder God Set created the Serpent Cartel to help support his rise. Various captains of industry melded in a psychic link after donning the power of the Serpent Crown. Sebastian Shaw joined Gregory Gideon, Leland Owlsey, Cornelius van Lunt and many others to secretly rule America after bringing the President under the Crown’s sway as well. The power of the Crown even brought Earth’s heroes the Squadron Supreme under their control. They mentally reached out to Hugh Jones, CEO of RoXXon on Earth-616 who wielded his own version of the Serpent Crown, to combine forces. This proved to be a mistake, for the Avengers of Earth-616 stole and disposed of Earth-S’s Serpent Crown. The Cartel lost their power over the Squadron and were soon deposed.
In the timeline of Forever Begins Yesterday, Sebastian Shaw was a commander in the Mutant Liberation Force, a collection of mutants and superhumans opposing the tyrannical rule of the Sphinx. He led an infiltration unit inside the force field of Maqaman Island, intent on destroying the power planet powering the field to bring it down entirely. Shaw’s team was opposed by Captain Assyria and the Avengers, but they were successful, allowing Magneto to bring the entire MLF into the city to battle the Sphinx.
In the Ultimate universe, Sebastian Shaw and the Hellfire Club represented a cult of Phoenix worshippers dating back thousands of years. Claiming to be a form of Illuminati, the Hellfire Club propagated Phoenix worship throughout all levels of society, even claiming the American Eagle was in actuality secretly a Phoenix. The Club provided secret support to Charles Xavier and his X-Men, because they believed the Phoenix God would be able to rise through the body of Jean Grey. Apparently a non-mutant in this reality, Sebastian Shaw initially kept his distance from Xavier to avoid telepathically alerting him to his donors’ true intentions. When the proper celestial alignment was nigh, however, Shaw and the Club invited the X-Men to attend a gala announcing these captains of industry openly supported the mutant race. Instead, the X-Men were captured and Jean was prepared as a vessel for Shaw’s god. Unfortunately for Shaw, he was successful. The vengeful god was furious at the mistreatment of its avatar and her friends. The Phoenix incinerated the Hellfire Club members and peeled Sebastian Shaw’s mind like a grape to transfer all his wealth to Xavier before melting him away too.
In What If...? (2nd series) #46-47, a falling out between the X-Teams led to increased rivalry among mutant factions. Sebastian Shaw recommitted himself to supplying Sentinels for Project: Wideawake in order to fill his pockets. However, when Magneto led the conquest of Washington, the President released the Sentinels unchecked and mutants were hunted in the streets. Even Shaw eventually fell to the anti-mutant riots. As he lay dying, though, Sebastian spoke to Wolverine and passed on the cloaking tech he had built into the Sentinels to protect the Inner Circle from their detection. The last generation of X-Men would have this small protection as they fought against mutant genocide.