Once a Mutate on the island nation of Genosha, Abyss was among many who contracted the deadly mutant-killing Legacy Virus. Professor Charles Xavier recruited Abyss into the Mutant Underground, a secret cabal of both mutants and pro-mutant human supporters fighting for the vindication of mutantkind, and assigned him as a bodyguard for Genoshan scientist Renee Majcomb who was researching a cure for the Virus. Secreted away deep in the Louisiana bayou, Abyss aided the mutant soldier from the future Cable, his mercenary ally Domino and the techno-organic alien Douglock in preventing First Strike soldiers from the anti-mutant taskforce Operation: Zero Tolerance from capturing Majcomb.
After a cure for the Virus had been released, Abyss found himself in Berlin battling the fire-wielding mutant Fever Pitch. Both were captured by the mutant X-Corps militia led by the former X-Man Banshee. While being held for scientific study, Abyss witnessed the murder of the Japanese mutant Sunpyre by rogue X-Corps members. Following the revelation that the shape-changing mutant terrorist Mystique had infiltrated the X-Corps in an attempt to seize its assets for her own use, a wounded Banshee freed Abyss from his confinement, allowing him to use his power to pull Mystique into the void within his body.
Later, Abyss was mentally compelled to travel to the Caribbean island of Isla des Demonas where he joined the X-Man Nightcrawler and other mutants with teleportation powers in creating a portal to the other-dimensional home of Azazel, a demonic-looking mutant from ancient times who was amassing an army with which to reclaim the Earth. The X-Men arrived to rescue their teammate, and inadvertently caused the collapse of the portal. Many of the teleporters were killed, but not before all assembled were transported through to the other dimension. There, Abyss' powers acted in reverse, ejecting everything the void within his body had ever pulled in, including Mystique. Azazel subsequently revealed that he was the father of the teleporters, collectively referred to as the Neyaphem, and sought to enlist the aid of Nightcrawler and Abyss in opening another portal to Earth. At that moment, back on Earth, the X-Man Polaris used her magnetic powers to force open the void within Abyss' body, allowing the heroes to return and leaving Azazel and his followers trapped.
Following the advent of House of M|"M-Day", Abyss was one of many mutants who were stripped of their mutant nature to become ordinary humans.