Author's Note – I do not own any of the characters, Marvel and DC do.
This is a sequel to The Institute Saga, story ID ( s/8891801/1/The-Institute-Saga ).
Of course, you can always go to my profile to find it…
Oh, anything ##written like this## is spoken Kryptonian.
What Has Gone Before
The sole survivor of an ancient race, Kal-El, son of the scientist Jor-El and his wife Lara Lor-Van, was sent to Earth as an infant mere moments before Krypton was destroyed. Discovered by Jonathon and Martha Kent, the newly-renamed Clark Kent was raised as a human by his new, loving parents.
Ater his father's death, Clark took his heritage and travelled to the Arctic where he activated the Fortress of Solitude and spent four years learning about his now-extinct race before returning to his mother's side.
Approached by Charles Xavier, Clark and his mother accepted places at the Xavier Institute for the Gifted, Clark as a tutor/mentor while his mother, by unanimous acclaim, became the goddess of the kitchen. Clark moved the Fortress, concealing it underneath the manor and using the technology in it to create defences that were effectively unbreakable, giving the inhabitants the knowledge that they were truly safe.
Joining the staff of the mansion, Ororo Munroe (Storm), Logan (Wolverine) and Professor Xavier himself, Clark soon befriended the two students already there, Scott Summers (Cyclops) and Jean Grey. More students soon came to the mansion to join them, the teleporter Kurt Wagner (Nightcrawler), Katherine Pryde (Shadowcat), Anna Kent (Rogue) and Ororo's nephew Evan Daniels (Spyke). At Logan's request, Clark helped to recover and heal Logan's old friend Steve Rogers (Captain America), who had spent several decades in cryogenic stasis.
Xavier's enemies were not idle during this time. While gathering powerful mutants to become his Acolytes, Magneto sent one of his lieutenants, the shapechanging Mystique, to gather younger mutants to counter Xavier's students. The four recruited mutants, Lance Alvers (Avalanche), Todd Polanski (Toad), Fred Dukes (Blob) and Magneto's son Pietro Maximoff (Quicksilver) became known as the Brotherhood. Although they faced off against Xavier's students several times, they soon settled into an uneasy truce until the day that Pietro betrayed Mystique at his father's orders, attempting to kill Superman as he did so.
Rescued from imminent interrogation and torture, Mystique officially (albeit temporarily) allied herself with Xavier's forces, reuniting first with her son, Kurt, then her one-time adopted daughter, Rogue. Her defection allowed Xavier to discover Magneto's plans and, with the aid of the Avengers, move to counter them.
Magneto's flawed plan to transform the population of Earth into Mutants using a Kryptonite-enhanced energy wave came within seconds of wiping out Humanity, but a new factor was introduced. Xavier's half-brother, Cain Marko (Juggernaut) was flung into battle by Superman and promptly seized the keystone of Magneto's plan, the Gem of Cyttorak, the very item that had empowered Juggernaut years previously. The resulting explosions destroyed Magneto's plan, but he managed to escape with many of his followers.
With the threat negated, the Avengers and the X-men returned to their own lives. The three remaining members of the Brotherhood (since Pietro had fled with his father) returned to Bayville in a stolen plane where they were met by Mystique, who decided to continue leading them, this time in a stance of neutrality.
Superman chose to use the respite (as brief as it may be) to go back to what was once his homeworld to see if there was anything left that he could claim as his birthright.
Juggernaut, freed from the induced rage of the Demon Cyttorak but still possessing its power, remains loose.