A 13-year-old John Hardesky was tricked by Nazis into spying on the Captain America project. Steven Rogers became Captain America as the first of a new breed of super soldiers who would improve America's chances of winning the war. However, the super soldier formula was destroyed by spies, and Reinstein was also lost in the ensuing explosion.
The Red Skull tried to make John Hardesky reveal the super soldier formula to him, Hardesky having memorized it with his photographic memory. However, Hardesky realised that they were Nazis and fled, vowing never to reveal the formula to anyone.
Despite the formula being destroyed, scientists were able to reproduce a less effective version of the serum, creating the Six American Warriors.
Andre Cocteau was employed in a team of scientists as a robotics engineer, to build the Red Skull an army of robots to assist the Nazis in World War II. However, Cocteau was actually an American spy, unbeknownst to Wolverine and Captain America who teamed up to save an allegedly kidnapped Cocteau. After being seemingly betrayed by the scientist to the Red Skull, who escaped with Cocteau, Wolverine and Cap considered the mission a failure. Cocteau later revealed his hidden agenda to the Red Skull and sabotaged the plot.
The Red Skull concocted a new plan to build a Doomsday Device. However, the skull and Captain America were both trapped in a vortex during a fight.
Keane Marlow, previously one of the Six American Warriors, enjoyed the thrill of using his super powers, and while attempting to stop a gang war his wife was killed in the crossfire. In order to ensure that he would never be tempted to use his powers again, Keane gave the ring which rationed his powers to friend Ben Parker, and told him to hide it. Ben hid it in his basement.
Erik Magnus, a Polish survivor of World War II which caused the loss of his entire family, began working in a hospital to treat other survivors. There he met Charles Xavier, with whom he teamed up to save survivors from attacking Nazi remnants using their super powers. While Magnus wanted to murder the Nazis, Xavier didn't condone violence, causing a rift between the pair who ceased their friendship.
Richard and Mary Parker sent on a secret mission to Russia after the "Doomsday Device" which threatened to destroy America, but allegedly announced that they were double agents working for the U.S.S.R. They then died in a plane crash.
As a result of his parents' death, Peter Parker was sent to live with his uncle Ben and Aunt May.
Rogue's powers put boyfriend Cody in a coma. She was rejected by her father, and taken in by Mystique, but eventually reformed and joined the X-Men.
Peter Parker bitten by a radioactive spider while in high school, and gained superhuman powers. He went on TV in a costume and under the alias of 'Spider-Man' and later went on to do wrestling. However, his refusal to stop a crook inadvertently caused the death of Uncle Ben. Peter then became a crimefighting superhero.
The X-Men discovered a Mutant Registration Program, used by a group of Sentinels to develop files on mutants to locate and destroy them. The X-Men managed to destroy the files, but Morph was apparently killed by the Sentinels and Beast was captured, put on trial and incarcerated. Sabretooth protested at the trial, resulting in him being shot, but the X-Men treated him and took him back to the X-Mansion, against Wolverine's advice due to his past experiences with him.
Erik Magnus, now under the alias of Magneto, attacked a military missile facility, hoping to launch nuclear missiles in order to ensure a war between mutants and humans. However, the X-Men countered the plot. Magneto subsequently destroyed a chemical plant to attract Professor X, who confronted him and forced him to recall his experiences of World War II, causing him to flee.
Sabretooth revealed his true colors to the X-Men, broke free and attacked Jubilee, but Wolverine saved her and fought him, resulting in Wolverine suffering deep wounds to his chest.
Morlock's kidnapped Cyclops and Jean Grey, but they were saved by the rest of the X-Men, including Storm who challenged the Morlock leader for membership of the group, but allowed Callisto to continue ruling the Morlocks after Cyclops and Jean were saved.
Wolverine travelled to Canada, and seeked solitude under a Inuit, but was stalked by Sabretooth, whom he defeated, saving the villagers, before returning to the X-Men.
The X-Men discovered that Genosha welcomes mutants as a tourist attraction, but whilst visiting Storm, Gambit and Jubilee were captured by a Sentinel, and forced to work as slaves on the island along with many other mutants, to build a Sentinel factory. Having escaped, with help from Cable Gambit attacked the Sentinel factory and saved the enslaved mutants. He, Storm and Jubilee escaped and destroyed the factory.
Juggernaut tried to get revenge on Professor X for their childhood, destroying the X-Mansion and robbing banks to get his attention. Colossus and the X-Men teamed up to stop him, and after having his helmet removed Juggernaut's memory was erased by Jean Grey. The X-Mansion was then rebuilt.
A doctor at the Muir Island Mutant Research Center claimed to have found a cure for the mutant gene. Rogue sought the treatment, but it turned out it was a plot issued by Apocalypse. The X-Men defeated Dr. Adler and Mystique. Warren Worthingon sought the treatment also, but was collected into Apocalypse's Horsemen, and joined them in devastating the planet. However, they were countered by the X-Men, and Rogue absorbed Archangel's memory, removing Apocalypse's control over him.
Earth-92131 was visited by Bishop from Earth-31393, a dystopian future.  Bishop arrived through a time portal to prevent the assassination of Senator Kelly, in order to change the devastating future he had witnessed. Bishop believed the assassinator to be Gambit, but in his future Mystique had impersonated Gambit when carrying out the assassination. Gambit caught the imposter and fought them, and Senator Kelly escaped assassination , but was kidnapped by Magneto, who wanted to carry out the kill himself due to Mystique's failure. The Sentinels then attacked Magneto and took Kelly, but the latter was ultimately saved by the X-Men.
Mister Sinister sent a brainwashed Morph (who had been revived after his death) to set traps to destroy the X-Men, at the same time of Cyclops and Jean Grey's wedding. However, the X-Men fought Morph and defeated the Nasty Boys on Sinister's island.
The Shadow King lured Storm home to Mt. Kilimanjaro by 'possessing' her young spiritual son MjNari, so Rogue and Storm travelled to Africa to stop the Shadow King. After a brief fight, MjNari lured Shadow King back into the Astral Plane and the Shadow King was once again trapped there.
Omega Red was resuscitated by three corrupt generals who wanted to reclaim and rule the crumbling old Soviet empire. Colossus went to the X-Men for help to save his country. The X-Men, however, were unable to stop Omega Red, but eventually managed to do so with the help of Darkstar. Omega Red reverted back to cryogenic sleep, and Russia was saved.
Alpha Flight captured Wolverine, demanding that he reveal the secret of his adamantium skeleton. Carrying out a series of tests on him, Vindicator subjected Wolverine to a great deal of pain, but decided to refrain eventually. Wolverine then defeated Vindicator, and warned his former comrades never to seek him again.
Gambit was forced to return to his southern roots by an ancient tithe, an old family feud and the kidnapping of his brother, Bobby. Bella Donna of the Assassin's Guild used the kidnapping to lure Gambit into her clutches and forced him into completing the aborted marriage. Upon trading Bobby and the tithe for Gambit, Bella gave the Thieves a fake tithe, ensuring their destruction at the hands of the X-Ternal. The other X-Men followed Gambit back to the bayou, and with his help they successfully confronted the assassins at the designated place and time and exposed their deception. When the X-Ternal came, Jean Grey forced a telepathic link with the X-Ternal, forcing her to see the truth. Realizing that she had been duped, the X-Ternal took away Bella's powers, and the X-Men returned home.
Earth-92131 was visited by Cable of Earth-13393, a future previously created by Bishop to alter his future timeline, but didn't work out and created a plague. Bishop therefore went back in time again to prevent the plaugue, but was attacked by Cable, who wanted to save his own future. After researching the X-Men's biography, Cable learned that he could use Wolverine's healing power to create the antibodies needed to preserve his future. Cable therefore saved both his and Bishop's timelines.
Mystique forced Rogue to recollect her past. Ms. Marvel's mind was trapped in Rogue's body after the latter absorbed her entire mind. In Rogue's mind, she and Ms. Marvel fought, but Jean Grey with help from Cerebro entered her mind and freed Rogue.
Beast fell in love with a blind woman named Carly, who was kidnapped by the "Friend of Humanity". Wolverine saved Carly by infiltrating the group and revealing to them that the leader, Graydon Creed Jr., was related to Sabretooth.
X-Men kidnapped by Mojo, who cast them in his television show in an alternate dimension. However, Longshot betrayed Mojo and helped them escape, after they destroyed the show.
Charles Xavier and Magneto visited Savage Land, witnessed Sauron kidnapping Shanna, before being captured and held as bait to lure the X-Men by Mister Sinister. Sinister planned to use the X-Men's genetics to take control of Magneto's band of mutates. After being captured with the rest of the X-Men, Wolverine escaped and teamed up with the native Ka-Zar who helped him to free the rest.
Wolverine lured to the Morlocks by his former love Yuriko, whom he helped discover an alien ship. However, it turned out to be deadly, and sucked the life out of Jubilee who followed along with Gambit. However, the X-Men used electricity to defeat the alien.
Jean Grey acquired the power of the Phoenix and the battle for the M'Kraan Crystal commenced. Jean sacrificed herself and trapped D'Ken in the crystal before soaring into the heart of the Sun.
Cyclops quit the X-Men while grieving over Jean Grey and returned to his old orphanage, encountering his friend Sarah. Cyclops saved her children from a man who claimed to adopt mutants but planned to use them to destroy humans in order to ensure mutant dominance. He then decided to rejoin the X-Men.
The Phoenix discovered to be alive by Charles Xavier who returned her to Earth.
Archangel tried to destroy Apocalypse, who he blamed for ruining his life. The X-Men helped him, but instead trapped Apocalypse in a force field and jettisoned it into outer space, despite being aware that he was bound to return.
Longshot chased by Mojo and entered the X-Men's dimension. The X-Men helped him and defeated Mojo once more.
Former X-Man Iceman tried to save his apparently kidnapped wife Lorna, but after infiltrating the compound with help from the X-Men discovered that she had willfully joined the X-Factor.
Storm kidnapped by Sauron and taken to Savage Land in an attempt to awaken Garokk. When awakened, Garokk fused with the island's volcano, but was defeated by Sauron who gained it's powers. Storm then regained control over her mutant powers and returned to the X-Men.
As a result of the Inner Circle Club's attempt to take over Jean's mind, the Dark Phoenix emerged and completely took over Jean's body, and attempted to destroy entire star systems. Eventually, the Phoenix was split from Jean who was revived in full human form once more, while the Phoenix disappeared into the stars.
Dr. Curt Connors became the Lizard after conducting an experiment to re-grow his lost arm. He was then saved and cured by Spider-Man after a fight.
Farley Stillwell transformed Mac Gargan into the Scorpion on J. Jonah Jameson's behalf. After almost destroying Spider-Man, Scorpion went on a rampage and threatened to destroy New York City after realising he had become a monster, but was stopped by Spider-Man, resulting in him being imprisoned.
The Kingpin forced Norman Osborn to have Spider-Man eliminated in order to pay off a debt. Norman hired Spencer Smythe to build robots to carry out the task, and in exchange Norman would build a hoverchair for Spencer's son Alistair. However, Spider-Man fought and destroyed the Black Widow Spider Slayer, and Spencer perished in an explosion at Oscorp.
The Kingpin found Spencer Smythe alive in the Oscorp wreckage, but placed him in cryogenic suspension, before approaching Alistair and telling him that Spider-Man was responsbile for his father's demise, suggesting that he build more Spider Slayer robots under a labatory provided by Kingpin. However, Alistair's robots were ineffective and Spider-Man destroyed them.
Cyclops discovered that Corsair may be his father. Corsair was on the run from Shi'Ar authorities, who demanded that Cyclops turn him over to them. However, the Shi'Ar police officers were corrupt and attempted to kill a witness under Corsair's protection. The X-Men defeated the corrupt Shi'Ar officers and Cyclops invited Corsair to stay for a while, hoping to clear things up, and Corsair accepted.
Spider-Man framed by Mysterio, who wanted revenge for ruining his life and causing him to go to prison. However, with help from Terri Lee Spider-Man cleared his name and defeated Mysterio.
Felicia Hardy kidnapped by Doctor Octopus, who held her and later J. Jonah Jameson hostage in an attempt to force her mother Anastasia to pay the ransom money he claimed to be owed for his dangerous experiments. However, Spider-Man saved the hostages and Doc Ock was imprisoned.
In a New Mexico desert, Wolverine witnessed the crash of a spaceship carrying horrific, alien bug-like creatures - the Family - which overwhelmed him. Rogue reunited with Cody, who was secretly part of the Family's plot to have Rogue become their new leader. The X-Men defeated the Family.
John Jameson accidentally brought the Venom symbiote to Earth in his shuttle, which crash landed on the G.W. Bridge. The Prometheum-X from the shuttle was stolen by the Rhino for the Kingpin. However, J.J. Jameson made out that Spider-Man stole it, and while he was agitated he was bonded to the symbiote in his sleep, and later discovered that it gave him great powers, but also that it increased his aggression. After nearly killing Rhino and Shocker, Spider-Man got rid of the symbiote, which then bonded with Eddie Brock, a man who blamed Spider-Man for his ruined life. Venom tried to destroy Spider-Man, and proved to be a relentless opponent, but Brock was de-tached from the symbiote by Spider-Man who had it flown back into outer space on a probe.
Juggernaut's life put at risk when someone else uncovered the Ruby of Cyttorak and claimed the powers of Juggernaut for himself, wanting to pick up girls. Cyclops and Wolverine found the new Juggernaut and intervened. He dropped the Ruby and Wolverine and Cyclops escaped with it. Professor X gave the Ruby back to his step-brother, restoring the original Juggernaut. He threw the Ruby into space and left the X-Men without a fight.
Omega Red, the destruction machine from the former Soviet Union and a sworn enemy of Wolverine, was thawed and sent two miles beneath the ocean to salvage a disabled, toxic nuclear submarine threatening to break up near Hawaii. His only condition: Wolverine and Storm go down with him as insurance. Once in the sub, Omega Red revealed his plan to use the missile to cause destruction. Rogue destroyed the sub, rendering it unable to launch its warheads. The submarine sank deeper into the ocean, leaving Omega Red trapped inside.
In Africa, Sergei Kravinoff became Kraven the Hunter after taking a wonder serum to save his life. Sergei went to New York but was stopped by Spider-Man. Sergei and Mariah Crawford returned to Africa again.
Weary of battling for mutant supremacy, Magneto offered to transport all mutants to an orbiting asteroid named Asteroid M where they could live peaceful and human-free lives; however, Fabian Cortez tricked Magneto into an escape pod and launched him into space. When the X-Men arrived to investigate Magneto's intentions, Cortez blamed Magneto's disappearance on them and accused them of assassinating Magneto. When the X-Men tried to escape, Gambit sacrificed himself and the other X-Men escaped.
As Magneto plummeted helplessly to Earth, Fabian Cortez assumed control of Asteroid M and sent hundreds of missiles towards Earth. Meanwhile, Rogue went to help the X-Men and tried to find the missing Gambit. Magneto freed himself and returned in time to destroy both the missiles and Asteroid M. Everyone escaped before the asteroid was destroyed and they all returned home (Gambit included) Meanwhile, Cortez was rescued from the descending asteroid by Deathbird and Apocalypse.
Hobgoblin hired to assassinate Wilson Fisk by Norman Osborn. However, Hobgoblin briefly betrayed Norman and allied with Kingpin. Hobgoblin then defeated the Kingpin and took over his empire. He was then stopped by Spider-Man, and the Kingpin reclaimed his empire.
When Professor X suffered a slight concussion, his powerful psychic mind was suddenly open to manipulation. The Shadow King took advantage of this and possessed Xavier, leaving his mind trapped on the Astral Plane. Jean Grey again trapped Shadow King on the Astral Plane, and Professor X regained control of his body.
The day Morph rejoined the X-Men, terrorists attacked a top-secret, high-tech weapons factory; the alert interrupted his homecoming party. Morph and Wolverine investigated and discovered that the Sentinels were back. Morph hesitated to fight the Sentinels, remembering getting shot by a Sentinel. Eventually, he overcame his fear and defeated them, but he left the X-Men in the end, saying he was not ready yet.
Chameleon tried to assassinate two diplomats at a United Nations conference held at the Daily Bugle. However, he was stopped by S.H.I.E.L.D. and Spider-Man, and incarcerated.
When Cyclops flied solo to a tiny, western, desert community to see an old friend, his plane was blasted out of the sky. Injured and unable to use his powers, he struggled into town, only to discover his friend was missing and the town caught in the grips of a militant, mutant-only, anti-human hate group: the Children of the Shadow. The Children of the Shadow hunted him down. When his powers returned, Cyclops got help from some mutants and defeated them.
Gambit, Rogue, and Wolverine took a ski trip to Germany. While Gambit and Rogue seemed to be enjoying themselves, Wolverine was restless, and longed for some action. When he heard reports of a demon hiding in a local monastery, his investigation revealed not a demon, but a mutant, Nightcrawler, whose devilish appearance was in stark contrast to his peaceful and deeply philosophical nature. Later the townsfolk attacked and burned the monastery. The X-Men convinced the townsfolk not to fear what they do not understand.
The Kingpin formed the Insidious Six, consisting of Chameleon, Scorpion, Mysterio, Shocker, Rhino and Doctor Octopus. Their purpose was to capture Spider-Man, which they easily succeeded in doing as Spider-Man had lost his powers. However, Spider-Man partially regained his powers and escaped, after which the six disbanded. Despite regaining his powers, Dr. Curt Connors carried out some tests on Spider-Man and revealed it was only start of a mutation process.
Earth-92131 temporarily replaced by Earth-95099 after a series of time-travelling events; In Earth-121893 in the year 2055, Fitzroy and Bantam travelled to Earth-95099 in the year 1959, to assassinate Charles Xavier. However, Bishop and Shard also travelled from Earth-121893 to Earth-95099 to counter the attack, but were unsuccessful. When Bishop and Shard travelled back to 2055, Earth-121893 had been replaced by another timeline (number?) as a result of Xavier's assassination in Earth-95099. Despite this, they travelled back to another past timeline (number?) and were able to prevent the assassination, restoring both Earth-92131 and Earth-121893.
Hydro-Man obsessively pursued Mary Jane Watson (who was at the time dating Peter Parker). Despite Mary Jane telling him that she didn't love him anymore, Hydro-Man refused to let her go. Spider-Man tried to stop him, but was overpowered by his water abilities. Mary Jane, however, led Hydro-Man to the top of a building, where he was too far away from any source of water, and evaporated.
Moira MacTaggert tried to help her son Kevin (Proteus), but when he escaped from Muir Island she called on the X-Men for help. Proteus, who had never been off the island before, wreaked havoc while trying to find his father. When he discovered that his deadbeat dad was a prominent politician, Proteus stormed the Union Hall right in the middle of his dad's campaign speech on 'family values.' Proteus told his father that he was his son, his father denied it and ran away in horror, crying for help. Angered at his father's reaction, Proteus created more havoc, but Professor X later calmed him down, and he stopped the rampage. Then he went back to Muir Island with Moira.
Spider-Man sought help from Professor X about his growing mutation, although Xavier told him that his job wasn't to cure mutants, but to help them accept who and what they are. Despite this, Beast told Spider-Man of Herbert Landon and the Brand Corporation, who had apparently found a cure for mutancy. However, it turned out that Landon's hidden agenda was to destroy all mutants, and kidnapped Beast, planning to annihilate him first. Spider-Man and Wolverine teamed up to save Beast, but they were distracted by the arrival of the Hobgoblin, who wanted to steal Landon's research. Hobgoblin caused Landon to fall into the mutant-toxic serum himself, before fleeing. By the time the X-Men arrived to assist Beast, Wolverine and Spider-Man, Landon had mutated into a large creature feeding off electricity. With help from a mutant called Genevieve, The X-Men and Spider-Man were able to stop Landon. Landon was returned to his human form (albeit with a mutated side to his face remaining), and hospitalized.
Shortly after Magneto broke into the X-Mansion, High Evolutionary and his New Men captured him, Quicksilver, Beast, Wolverine and Scarlet Witch, to do experiments on them. He also revealed that Magneto was Quicksilver and Scarlet Witch's father. The other X-Men later defeated High Evolutionary and His New Men, saving the captured mutants.
Nightcrawler received a mysterious message, informing him that his birth mother (whom he never knew) was in trouble, and turned to the X-Men for assistance. Jubilee was baffled that Nightcrawler wanted to help the mother who abandoned him. Nightcrawler admitted there had been pain, but his faith in God helped him to overcome her rejection.
Dr. Mariah Crawford developed a cure for Spider-Man's disease. Meanwhile, Michael Morbius unintentionally came into contact with a sample of Spider-Man's mutated blood. Just after, Morbius was bitten by a vampire bat, and was transformed into a vampire-like creature himself, feeding off plasma. Spider-Man took the serum given to him by Dr. Crawford, but took it too early against her advice, resulting in the serum advancing his mutation and causing him to grow four extra arms.
As Morbius drained the plasma of many victims, Spider-Man was blamed by the media for the attacks. This alerted the attention of the Punisher, who sought to capture Spider-Man for his "menacing ways". Punisher tracked Spider-Man to a warehouse, where the latter's mutation advanced further and he transformed into a gigantic, humanoid spider. Punisher continued to hunt the mutated Spider-Man, but was ambushed by Sergei Kravinoff, who wanted to help Spider-Man on behalf of Mariah. The Man-Spider was eventually given a serum by Mariah to return him back to normal. Nevertheless, Spider-Man required to take the serum every twenty-four hours to keep him from mutating again.
Wolverine, losing control, quit the X-Men and returned to the rural Japan of his younger days, in an effort to find himself. He worked peacefully with a former spiritual teacher, the monk Oku, to build a temple. However, the neighboring village was about to be attacked by bandits, led by the merciless Silver Samurai, unless payment was made. Some of the villagers wanted to resist, and asked Wolverine for help. Wolverine was torn, as it was just the sort of thing he had wanted to leave behind. Nevertheless, Wolverine defeated the Samurai and saved the village, before deciding to return to the X-Men.
A cryptic postcard unleashed a flood of maddening and painful memories in Wolverine that threatened to drive him insane. To keep his mind from being torn apart, Wolverine and Beast travelled to the one location that may have held the answers to his hidden past: the ruins of the top-secret Weapon X lab where Wolverine's bones were laced with adamantium. There they encountered other former 'test subjects'—Sabretooth, Maverick and Silver Fox—who were suffering similar mental breakdowns. Later they discovered that many of their memories were implanted, and their true memories were destroyed with the lab.
Christmas Day Jubilee, Storm and Wolverine went last-minute shopping in Manhattan, only to be caught in a life-or-death crisis involving Leech, the littlest Morlock. Leech required blood transfusion, so Wolverine's blood was given and then Leech recovered. Additionally, Storm agreed to give back to Callisto her title as the Morlock's official leader.