Author's Note – I do not own any of the characters, Marvel and DC do.
This is a sequel to The Institute Saga III (as you may have guessed from the name)

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Prologue

What Has Gone Before (Part One)

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)

Using the lack of obvious threats to perform a mission of his own, Superman traveled 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…

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What Has Gone Before (Part Three)

With the newest threats apparently suppressed, the Institute started to return to normal, only for things to be shaken up when an alternate version of Superman appeared from a different reality. After managing to help him return to his home (which necessitated building an inter-reality Gate), the X-Men managed to revive four of the remaining six Kryptonians that had been rescued from Argo. Soon after, Superman and Mystique prepared to get married in a ceremony shared with Reed Richards and Susan Storm. However, once again events proved a hindrance.

Partway through the ceremony, a starship commanded by General Zod and carrying over fifty of his men appeared in orbit. Only a show of strength and the offer to let them transform Venus into a new homeworld for the Kryptonian refugees dissuaded the newcomers from trying to seize control of Earth. With the crisis averted, Superman and Mystique finally got married and went on their honeymoon.

Magneto had not been idle and took the offensive using Galatea, a clone grown from Kara's QNA, to try and kill General Stryker, a military man known to believe that mutants were a threat. Soon after, Magneto reacted to the news that a Cure for mutation had been found by gathering a veritable army of mutants and striking at the source of the Cure. His assault came within moments of succeeding, but the timely arrival of the X-Men proved to be the tipping point. However, during the battle, Angel was struck down from the skies by Galatea. The clone was in turn struck down by an enraged Ororo Munroe who used a lightning bolt of unprecedented power to avenge her winged friend.

Just prior to these events, Superman had left Earth at the behest of the son of Odin, leading a group of the most powerful heroes on Earth against the Mad Titan Thanos, who was in the process of collecting the Infinity Gems, metaphysical constructs that would grant him infinite power when used in conjunction with a special gauntlet. As Thanos placed the last of the Gems into the Gauntlet, the heroes attacked with Squirrel Girl being the one to bring down the would-be Deity.

Both events were nothing more than diversions, however, hiding the true threat, the re-awakened ancient mutant known as Apocalypse. Moving in secret, the immortal being assembled a force of his own, using mind-controlled mutants, magical golems and subverted Sentinels to prepare for his planned assault. By his side stood the enigmatic Mr. Sinister while the four beings known as his Horsemen were ready to obey his every command. Controlled by technology taken from the Eternals, Magneto, the renamed Archangel, Galatea and the shapeshifter once named Morph and now called Apophis were extensions of Apocalypse's will. His forces were bolstered by those of Hydra, led by the Red Skull, his service ensured by the mental commands placed by Mr. Sinister decades prior.

Seeking to seize ultimate power on Earth, Apocalypse struck first at SHIELD, taking the three powerful Helicarriers that had just finished constuction. Even as he rode his new flagship into the skies, the heroes mustered their forces and struck back with Superman taking on Apocalypse in single combat, only to fall before his might.
Before Apocalypse could strike down the Man Of Steel, though, a new force entered the battle. General Zod and his two lieutenants came to the aid of Earth and defeated Apocalypse, imprisoning him within a stasis field. Without the ancient tyrant to lead them, Apocalypse's forces fell apart and were defeated, his Horsemen freed from his control.

Of the Four, Archangel chose to remain with the Gargoyles until he was sure he had healed. Magneto was rescued by Quicksilver and taken into hiding while Galatea awoke to find herself being offered a job with the Guardians of Genosha, a position that she accepted. Morph returned to the Xavier Institute where with the aid of Xavier and Sage, he began to heal from that which had been inflicted upon him.

Knowing that SHIELD had been compromised, Nick Fury called for help from his other-reality allies in weeding out the traitors while simultaneously overseeing the relocation of SHIELD itself into a new building created by the New Kryptonians. Although temporarily unable to counter the rising tensions once more, Fury was able to direct Generation-X and The Brotherhood into recapturing a former SHIELD base that the newly-founded Church of Humanity had seized, a base which was promptly sold to Xavier for use by Generation-X and the other students of the Xavier Institute.

And so with the threat of Apocalypse ended, the heroes returned to their lives.

However, they were unaware that a threat from the days of Krypton was closing in on them…

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monitoring program gaq59818ktm report indicates energy emissions similar to those of the krytonian embassy t-space power cores.

analyzing.

possibility exists that readings are result of technology carried on vessel sent from krypton just prior to cessation of planetary existence. analysis of records indicates high likelihood of craft containing single survivor of krypton. cross-referencing with population database… highest probability craft occupant is kal-el, son of jor-el.

conclusion – krypton is not completely recorded. action must be instigated to correct flaw.

alert – core programming forbids active termination of kryptonian citizens…

calculating solution…

monitoring program gkm68349zyh report indicates existence of planetary datanet.

analyzing.

planetary datanet protocols analyzed and integrated. scanning datanet search parameter kal-el

records found – 16928549

sorting via popularity – scanning record kal-el on datasite wikipedia

scanning…

scanning…