In the alternate timeline called Days of Future Past, Banshee had been maimed in an unknown incident, his left eye covered by a patch and his left hand missing, replaced with a bionic hand. Regardless, Banshee was the leader of a new team of New Mutants. Though set in the future, this group apparently came from a time before the Sentinels' final push to overthrow North America and placed it under their rule. Among Cassidy's future students was their team leader, Franklin Richards, a young Rachel Summers, a horrific Doug Ramsey, consumed by Technarchy matter and calling himself the Magus, the apparent daughter of Nightcrawler named Blue, and two other unfamiliar mutants. The final fate of these New Mutants is unknown, though considering Rachel and Franklin ended up in the camps and Sean Cassidy’s name was seen on one of the stones at the mass graveyards, the outlook is grim.
Banshee also played an important part in the X.S.E. future that Bishop is from. Though the time-displaced X-Man didn’t know any details, having originating from some 80-90 ahead in time and most records of the past having been lost, Bishop told Banshee that among the X.S.E. it had always been rumored that Banshee had been the last hope and the custodian of the next generation of mutants.
In the Age of Apocalypse, Banshee was also fighting for Xavier's dream. As one of the senior members of the team, at least in terms of age, Sean alluded to having been retired for a time and having only recently returned to the fold at Magneto's request when the X-Men attempted to go back in time and change the timeline. Oddly enough, he seemed to be Quicksilver's official second-in-command, as opposed to Storm, who was also on the team. After the X-Men had a few run-ins with Apocalypse’s Horseman Abyss, Banshee decided to let himself be consumed by him to use his sonic scream at him from within the void. Although it meant sacrificing his own life, Banshee took Abyss along, knowing that there was at least one less evil person in their world. It seems likely that, in this reality, Black Tom Cassidy was killed years before he could reunite Banshee and his daughter, as Sean seemed to have no idea of Theresa’s existence.
Banshee resided in the Realm of the Dead in the Earth X reality, having died during a conflict with Black Tom. Strangely, in the afterlife, the color schemes of costumes and clothing were reversed and everyone thought that they were still alive and that the people not there (those really alive) were the ones who had died. When Mar-Vell tried to overthrow Death herself and gain control of the realm, Sean was among his earlier recruits. With Death destroyed, a new Paradise was created; Sean's fondest wish was to spend the rest of his life in peace with his wife, Maeve, and for them to together raise their daughter, Theresa. Apparently, in the world of the living, Sean’s passing was apparently not widely known, as Mephisto was able to infiltrate an X-Men reunion disguised as an elderly Sean. It wasn't until Jean informed Scott through their psychic link that Banshee was with her in the afterlife that the devil was uncovered.
Ten to fifteen years in the future, the X-Men met their End when several of their deadliest foes banded together and attacked them from simultaneously on various fronts. During an attack by a group of Warskrulls, Banshee was revealed to have been killed and replaced by one of the aliens. The imposter’s mission was not fully revealed, though he might have been sent to get close enough to X-Men’s resident telepath, Emma Frost, to take her out before suspecting an attack.
In the altered reality of the House of M, Banshee was a member of the Marauders, a team of bounty hunters. Led by Callisto, the Marauders tried to hunt down Nocturne, as genetic scans revealed her to be related to Magneto. The Marauders even fought the Braddocks, the royal family of Great Britain, to get to their target, but they underestimated Nocturne’s powers. Using her possession talent, she took over Banshee and began attacking the remaining Marauders with Banshee’s sonic scream.
In one reality, the Apocalypse Twins, Eimin and Uriel, succeeded in their plan to destroy the Earth and relocate all of mutant kind to another world, though Uriel was killed. On this mutant utopia, called Planet X, Banshee served as one of Eimin’s Horseman of Death for years. He also served as jailor for some of the Avenger’s Unity Squad members they had captured, Wolverine and Sunfire. When the surviving Unity Squad members rescued their friends, Banshee tried to fight his brainwashing but ultimately failed, and Sunfire burnt him to a crisp. The surviving Unity Squad members were then successful in traveling back in time and erasing this future from occurring.