Author's Note – I do not own any of the characters, Marvel and DC do.
This is a sequel to The Institute Saga II (& Side Stories), but I'm sure you already knew that.
I'll be posting chapter a week, but starting you off with two (Including this one).
Enjoy!

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Prologue

What Has Gone Before (Part One)

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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.

After 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, returned to Earth.

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What Has Gone Before (Part Two)

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Using the lack of obvious threats to perform a mission of his own, Superman travelled to the ruins of Krypton where, as well as multiple pieces of salvageable technology, he also discovered nine surviving Kryptonians on Krypton's sister-planet Argos, held in stasis. Bringing them back to Earth, Clark met with the new students recruited by Xavier before encountering Squirrel Girl. Shaken by the experience, Superman brought his cousin Kara Zor-El out of Stasis. Soon after, the newly-named Supergirl aided Captain America in attempting to stop a plot by Magneto. Although they were less than successful, they worked together well enough that Kara afterwards accepted the offer of membership into the Avengers.

During a mission conducted at the same time, the other Avengers discovered that a female clone of Wolverine had been created. Programmed to be an assassin, the mutant known only as X-23 was handed over to Xavier and placed in a modified training room while Xavier and Jean Grey worked to undo the mental damage wrought upon her.

The tattered cloak of secrecy surrounding the existence of mutants was torn asunder when the anti-mutant and anti-alien group calling themselves the Friends of Humanity unleashed a weapon that they had been building in secret, the hunter-killer Sentinel robots. The first public outing of the Sentinels was in response to a crisis that the FoH themselves had created but the outcome they desired was prevented by the actions of the X-men, rescuing the mutant that the FoH had kidnapped and forced to go on a rampage. Soon after, over a hundred Sentinels were sent to wipe out the mutant-friendly nation of Genosha. The Genoshans, led by Juggernaut, fought back, aided by the X-Men. Unbeknownst to them, a second wave was destroyed by Magneto and his newest Acolyte, a less-than-perfect clone of Superman called Bizarro while the other two groups which descended on Bayville were taken out by Squirrel Girl. Soon after, the non-human nocturnal sentients called the Gargoyles sought an alliance with the X-Men and the mutant group calling themselves the Morlocks accepted an offer of refuge in the aptly-named undersea dome Sanctuary.

In an attempt at getting revenge, the anti-mutant Senator Kelly leaked Superman's true identity to the public. This backfired when several of the mutants at the Xavier Institute also chose to go public, gaining popularity due to their links to Superman. The plans of the Friends Of Humanity took another hit when Magneto and his Acolytes located and seized their main Sentinel factory, reprogramming the giant robots for a new mission, an assault on the White House.

Timing the attack for when the Avengers were dealing with a problem in Asgard, Magneto led his new metal soldiers and the clone of Superman named Bizarro in an attempt to seize the President. Despite Bizarro fighting Superman, the Sentinels found themselves outmatched by the X-Men and the other mutants who had rallied to their call and were destroyed. Magneto himself was almost killed in an explosion, but was rescued by his son, Quicksilver.

However, the attack was not Magneto's only plan, just the only one that had failed. His Acolytes managed to seize the lab belonging to the mutant scientist Mr Sinister and also managed to kidnap Susan Storm, delivering her to Latveria. The Brotherhood promptly teamed up with the Fantastic Four to rescue her, with several members of the X-Men and their allies aiding them in launching their assault and retrieving the Invisible Woman. Upon returning to the Institute in triumph, Clark proposed to Mystique.

Magneto and Doom, however, were far from defeated…