2001
A young mutant named Marie D'Ancanto manifests her powers, which cause her to drain the life force of anyone she touches. Horrified by this, she runs away from home, and eventually stumbles upon Logan fighting in the Albertan wilderness under the Wolverine name. Meanwhile, Senator Robert Kelly attempts to pass a mutant registration act that would require any and all mutants to reveal their identities and powers.
In the midst of the applause, Xavier, who was in the crowd, spots Magneto walking away. He goes to confront him, and after a short conversation, Magneto leaves. Meanwhile, Marie, calling herself Rouge, stores away in the back of Logane's truck, and when he discovers her, he initially tries to leave her but eventually decides to go back and let her come with him.
During their truck ride, the two begin to form a father daughter relationship. However, they are attacked by Saberooth, who had been sent by Magneto to capture Rogue. Logan defends her, and Sabertooth is forced to retreat once two of Xavier's X-Men, Scott Summers and Ororo Munroe, codenamed Cyclops and Storm respectively, arrive and help Logan.
Logan and Rouge are then brought to Xavier's school for gifted youngsters, where Charles tells Logan that Magneto had taken an interest in him. Rouge enrolls at the school, and meanwhile Senator Kelly is kidnapped by Mystique and Toad and brought to Magneto's island base of Genosha.
Magneto tests a mutant conversion machine he had created on Kelley, which succeeds, but Kelly manages to use his new mutant powers to escape. Meanwhile, Logan and Jean Gray get to know each other, and Logan and Cyclops begin fighting over her. That night, Wolverine has a brief nightmare about his time at weapon X. Rouge tries to wake him, but Logan accidentally stabs her out of instinct.
Luckily, Rouge is able to absorb his healing powers and heal herself, but that next morning Mystique, disguised as the mutant Bobby Drake, convinces her to run away. Xavier uses his telekinetic amplification device to locate Rouge, and learns that she was at a train station. Logan steals Cyclops's bike to get to her, while Mystique sneaks into the school and sabotages Cerebro.
When Logan finds Rouge he manages to convince her to return to Xavier's school, but Magneto, Toad and Sabertooth suddenly arrive to take Rouge, Magneto subduing Logan with his magnetic powers and taking Rogue. Meanwhile, Senator Kelly arrives at Xavier's school, and dissolves into a puddle of water once his mutation becomes unstable.
The X-Men learn that Magneto planned to use Rogue's power on himself to power the conversion machine. Charles attempts to use cerebro to locate Rouge, but thanks to the earlier sabotage, he gets put into a coma. Jean then fixes the device and uses it to locate Magneto and Rogue atop the Empire State Building. Magneto was planning to use his machine on world leaders who were meeting for a summit on the nearby Ellis island.
The X-Men quickly make their way to Liberty Island and begin battling the Brotherhood, with Logan defeating Mystique and Storm killing Toad. However, Magneto and Sabertooth manage to trap the group with metal cuffs, and Magneto then transfers his powers to Rouge, forcing her to use them to start the machine.
Logan manages to escape his bonds and engages in a brief fight with sabertooth, but is thrown off the statue. Luckily, he manages to cling on and jump back up. Cyclops, with Jean's help, manages to blast Sabertooth off the statue, and Storm and Jean manage to use their powers to get Logan to the top of Magneto's machine.
With time running out, Logan attempts to stop the machine and save Rouge, but Magneto, who had regained some of his power, stops him with his magnetic powers. However, this gives Cyclops a clear shot at Magneto, managing to wound him and allowing Logan to destroy the machine. He then places his hand on a dying Rouge's face, and transfers his healing powers to her.
Afterwards, Charles awakens from his coma and sees Mystique impersonating Senator Kelly on a live broadcast. He then sends Logan to Alkali Lake to try to help him learn about his past, and plays chess with Magneto in his plastic cell, telling him that his X-Men would always be there to stop him.
2 weeks later, as Logan stops to fuel Cyclops's motorcycle that he had stolen for his trip, he discovers Sabertooth following him. The two fight, with Logan defeating him and preparing to kill him until he sees Sabertooth's dog tags. Confused, Logan asks Sabertooth how he had it, and Sabertooth explains that he had always had it.
The two head to a bar to get drinks and talk, but are soon accosted by members of a terrorist group named HYDRA (Comprised of members of Red Skull's terrorist group that escaped prison) working for William Stryker, who had orders to bring in Sabertooth. The two mutant brothers fight together with great teamwork, but are eventually brought down. They eventually wake up in a helicopter and Sabertooth throws Logan off of it, saving him.
Sabertooth is then brought to a covert base to be experimented on by weapon X scientists, but as Stryker had predicted in 1979, the adamantium they tried to graft onto his skeleton is rejected by his body, so HYDRA executes him with Stryker's adamantium bullets. 2 weeks later, a mutant named Kirk Wagner is abducted by Stryker's forces, tortured, and placed under Stryker's control.
He is then sent to kill the recently elected president Mckenna, but is defeated by the presidential aides, teleporting away after getting shot in the arm. Mckenna then gives Stryker the authorization to attack Xavier's school, which he had learned about thanks to interrogating Magneto. Meanwhile, Logan finally reaches Alkali lake, only to find the facility long since abandoned.
He returns to the school, and asks Charles to show him more about his past, but Charles tells him that it was something he would have to find out for himself. Afterwards, Logan is forced to "babysit" the students while Xavier locates Nightcrawler and sends Storm and Jean to retrieve him. They find Nightcrawler praying in a church and convince him to willingly come with them.
Meanwhile, Cyclops and Charles visit Magneto in order to find out if he had anything to do with the attack on the president. Xavier reads his mind and learns of Stryker interrogating him about cerebro. As the two talk, a trap is sprung and Charles and Scott are captured. Meanwhile, Stryker and his men attack the school and abduct a few students. Logan and a mutant named Colossus round up a number of students and Logan defends them by killing the attackers, but he sees Stryker leading them.
Stryker is surprised to see Logan in the mansion, but he tells him that he knows much about him and asks for him to come with the military to discuss it. Before Logan can get any answers out of him, the young mutant Bobby, AKA Iceman, erects an icewall to allow the mutants to escape. Wolverine, Rouge, Iceman and another mutant named Pyro take Cyclops's car and head to Iceman's family in Boston to stay there until they could contact Storm and Jean.
Meanwhile, a few hours later, Xavier awakens and faces Stryker and his mind controlled assassin Lady Deathstrike. Xavier and Stryker have an argument, mentioning how Stryker's son Jason had been applied at Xavier's school, but when Stryker had learned that Xavier was teaching him to embrace his mutation, he withdrew him.
After Jason had tormented his parents to the point of his mother committing suicide, Stryker had put him in suspended animation until 2000, where he lobotomized him. Xavier realizes that Stryker had been controlling Nightcrawler to attack the president, and is then influenced by Jason Meanwhile, Mystique injects one of Magneto's prison guards with iron, allowing Magneto to escape and kill the guard.
As this happens, Logan's group reconvenes with Jean, Storm and Nightcrawler at Bobby's house in Boston. However, as they fly back to the mansion in their X-Jet, they are shot at by fighter planes, but saved by Magneto. Magneto tells them everything, including telling Logan that Stryker had been the one to implant him with his adamantium skeleton and wipe his memory. Jean then reads Nightcrawler's mind and learns that Stryker was at Alkali Lake.
They head there, and Mystique manages to infiltrate the base and get everyone in while disguised as Logan. Magneto and Mystique go to deactivate Cerebro before the brainwashed Xavier can use it, while Storm and Nightcrawler free the captured students and Jean fights a brainwashed Cyclops. Their battle manages to free Cyclops, but this damages the dam, which begins to rupture.
Logan finds Stryker in the lab where he was given his adamantium skeleton, and kills Lady Deathstrike in battle. He chases Stryker to a helicopter pad and chains him to the helicopter's wheel, while Magneto stops Cerebro and had Mystique impersonate Stryker so she could command Jason to have Xavier kill all humans. The two then flee aboard a helicopter alongside Pyro, who had been convinced to join Magneto's side.
Nightcrawler manages to teleport Storm inside of Cerebro, where she distracts Jason and sets Xavier free, the 3 then escaping afterwards. As Logan leaves, he takes a final look at Stryker and throws away his dog tags, leaving Stryker to die as he rants at him. However, the X-Jet malfunctions, and Jean seemingly sacrifices herself to buy enough time for the X-Jet to take off as the dam finally bursts.
Stryker and presumably everyone else still there are disintegrated by the water pressure. Shortly after these events, President Mckenna prepares to give a speech on the mutant threat, but everyone suddenly stops except him and the X-Men give him files on Stryker. Xavier warns him that humans and mutants must work to make peace.
Before the end of the year, the U.S government contracts Trask Industries to build a mutant detention center in Guantanamo bay known as Camp X-Ray. The camp is meant for mutants dangerous enough to be considered threats to natural security, and was formed in direct response to the recent mutant attacks.
2002
An 18 year old Peter Parker runs after his bus while everyone mocks him, them being on a field trip to the science department of columbia university. After some harassment on the Bus, Peter meets up with Harry and attends a demonstration of the institute's spiders with him. However, one of the super spiders ends up biting Peter, giving him Spider-powers.
After dropping off Harry and having a brief talk with Peter, Norman Osborn demonstrates Oscorps's glider technology and performance enhancer formula to the Oscorp board of directors and general Slocum of the US military. Doctor Mendel Strom informs Slocum about the unstable testing and the side effects of the enhancers.
Slocum threatens to pull funding from the enhancers and to give it to Oscorp's rival Quest Aerospace if the testing on the performance enhancers isn't completed in 2 weeks time. That evening, Peter returns home from his field trip and collapses on his bed from the effects of the spider-bite. That night, a desperate Norman tests the performance enhancer on himself, being driven insane by it.
He kills Doctor Strom and steals the glider tech, and the next day Peter wakes up to find impressive muscles that he had developed thanks to his powers. He slowly discovers his powers in moments like when he kicks the crap out of Flash Thompson, humiliating him. He skips the rest of school and discovers the rest of his powers, consisting of wall crawling, enhanced speed and agility, and organic webbing he could shoot from his wrists.
Peter ends up losing track of time, and when he returns home, he realizes that he had forgotten to help paint the kitchen with Uncle Ben after school. While taking out the trash that night, he hears Mary Jane and her father arguing, hearing her father's verbal abuse. The two begin to talk about their dreams beyond high school, with MJ mentioning her aspirations in acting, giving Peter a hint to her true personality.
Flash then comes to pick up MJ in his new car, inspiring Peter to gain money for his own car to impress MJ. Deciding to make the money through underground wrestling, Peter begins working on costumes for the match, and hones his skill for the next several days. At the same time, two thieves named Flint Marko and Dennis Caradeen begin planning to rob the fight promotor's money. When the day of the match arrives, Peter comes up with the excuse that he was going to the library.
Ben offers to drive him there and in the car they talk about his changing attitude and all the fights he was getting into at school. Ben tells Peter that with great power came great responsibility, only for Peter to tell him that he needed to stop pretending to be his father. Defeated and hurt by these words, Ben drops Peter off, who goes to sign up.
Donning a costume and calling himself the human spider, Peter easily defeats his opponent Bonesaw Mcgraw in a cage match, but is ripped off by the fight promoter who gives him 100 dollars instead of the 3000 he was promised. As Peter walks out in frustration, he sees Dennis Caradeen run off with the fight promoter's money, with Peter letting him so he could get payback.
Meanwhile, Ben arrives at the Library to pick Peter up, but Flint Marko coaxes him out of the car. He tries to steal it, but Ben tries to talk him out of it. Dennis rushes out towards his partner and causes Flint to accidentally pull the trigger, fatally wounding Ben. Caradeen abandons Flint and steals Ben's car to get away, leaving Flint with the dying Ben.
Flint flees the scene as the police discover Ben, and Peter follows the cop cars to him. Peter rushes over to him, but he dies in his arms as the police lock on to Dennis's location. Putting on the human spider suit, Peter chases the car to an abandoned warehouse and confronts Caradeen out of anger. Terrified, Dennis ends up slipping and falls to his death.
The cops below notice Peter and believe him to be the second convict in Ben's homicide, forcing Peter to flee. Later that night, Flint Marko is tracked down by the cops and placed into custody. Due to him being tied to Dennis Caradeen, who at the time was believed to be Ben's killer, Flint's wife Emma divorces him.
A few days later, Norman, now wearing a goblin-like exosuit and later referred to as the green goblin, attacks the Questerospace bunker. Attending an exoskeleton test, General Slocum is killed alongside other scientists and the funding for Oscorp doesn't get pulled due to this tragedy. A little over a month after Uncle Ben's death, Peter and Harry finally graduate high school and see MJ dump Flash, who had proposed to her.
At home, Peter gets rid of the human spider suit, vowing to live up to Ben's words focusing on great power and great responsibility. He fashions a new costume and formally becomes the hero Spider-Man. Peter starts off small at first, taking down muggers, car jackers and any crime he can prevent. After slowly revealing himself to the public, people begin to adjust to the fact that there is now a web slinging vigilante protecting them.
Many believe Spider-Man to either be a myth or some sort of creature, but most people agree that he must be a mutant. When the X-Men hear of Spider-Man, they also assume him to be a mutant due to his powers. Charles Xavier uses Cerebro to make sure that Spider-Man was a mutant and could be trusted, and thanks to this he learns that Spider-Man was Peter Parker and not a mutant.
Surprised at this, the X-Men ultimately decide to leave him alone, not wanting to get him involved in their affairs when he didn't have to be. The newspaper company the Daily Bugle, owned and run by J Jonah Jameson, tries to capture pictures of Spider-Man to keep their paper afloat, but ultimately have no luck. During this time, Peter and Harry move into an apartment that Norman let them live in upon moving into the city.
Meanwhile, Mary Jane, now working at the moondance diner, gets in contact with May, hoping to get Peter's phone number and address. She goes to his apartment to talk with him but runs into Harry instead, going to dinner with him instead and sparking a relationship with him. Peter later runs into MJ and learns about this relationship, which Harry had been keeping from him.
Later that day, Peter is offered a job by Norman at Oscorp, but he declines and is instead suggested to try getting a job at the daily bugle. Beginning to take photos of himself as Spider-Man, Peter gives them to J.Jonah Jameson, who hires him as a freelance photographer because of his incredible Spider-Man shots.
With the Daily Bugle now the best source for Spider-Man news, Jameson begins to slander Spider-Man as a menace on the front page. Around a month later, Oscorp had officially surpassed Quest Aerospace as the #1 supplier for the US military since the Goblin's attack had destroyed their prototype exosuits, which were worth millions of dollars.
However, Quest Aerospace would restructure and purchase Oscorp to prevent them from swallowing them in the future, and the board of directors agreed. When Norman learned about this, he was enraged. Around 30 days later at the third annual world unity festival, he arrived on the scene as the Green Goblin and killed the Oscorp board of directors with his pumpkin bombs.
Before he can kill anyone else, Peter, who had been there taking pictures for the bugle, quickly suits up as Spider-Man and fights the Goblin. MJ, who was also at the festival, is caught in the crossfire. Goblin escapes from the fight and Spidey rescues MJ, taking her away from the danger.
He drops MJ at a roof garden near Rockefeller center, and MJ begins to develop a crush on him, much to the disapproval of Harry. By this point, Norman, who had been struggling with his split personality of the goblin, vows to turn Spider-Man to his side, believing him to be a potential threat in the future.
Later at the Daily Bugle, Jonah gives the Goblin his name just as he attacks the Bugle, looking for Spider-Man's photographer. He interrogates Jameson, and when Spider-Man steps in to save him he is gassed with a paralysis mist and kidnapped. That night, Spider-Man wakes up and the Goblin tries to convert him to his side.
He tells Spidey that the public would eventually hate his stunts as a hero, and while he initially refuses, Goblin gives him time to think about it as he flies off. The next day, J Jonah Jameson paints Spider-Man as a menace working for the Green Goblin, and the city begins to divide on whether Spidey was a hero or not.
Peter meets MJ at her first audition that night, and as Spider-Man, saves her from some muggers as she was walking home. Afterwards, the two share a kiss with Spidey hanging upside down. 4 months later, Spider-Man is ambushed by the Green Goblin while saving people from a burning building, and gets cut on the wrist in the ensuing fight.
After the Goblin escapes, Peter returns to his apartment for Thanksgiving Dinner, with Aunt May, Harry, MJ and Norman all arriving to join in the festivities. Norman sees Peter's cut from the burning building fight and realizes that he was Spider-Man, causing him to leave in a hurry and insult Mary Jane in the process.
Everyone ends up storming out of the apartment after this, much to May's sadness. Now knowing Spider-Man's identity, Norman struggles against the Goblin personality, but ends up vowing to attack Peter's loved ones. He first attacks Aunt May, causing her to be hospitalized due to falling into shock.
At the hospital, Peter realizes that the Goblin knew who he was. He stays next to Aunt May studying for his college classes, and the next day MJ visits to talk with Peter as Aunt May pretends to sleep. MJ tells Peter that she didn't love Harry, and had developed a crush on Spider-Man. Peter tells her that he often talked to Spider-Man about her.
The two end up holding hands, but it's at that moment that Harry comes in with flowers, seeing the moment of compassion between them. That night, Harry returns home and tells Norman that he was right about Mary Jane not loving him. He tells Norman that Mary Jane loved Peter, giving Norman the idea of attacking her next.
He kidnaps MJ as the Goblin, and when Peter tries to call her, Goblin tells him to come to the queensborough bridge. Peter quickly suits up and swings to the bridge, and the final fight between him and the Goblin commences. The Goblin drops both MJ and a railcar full of children off opposite sides of the bridge.
Spidey manages to save both MJ and the children, even getting some help from New York's citizens in the process, but the Goblin decides to take the fight somewhere more private. He drags Spider-Man to an old abandoned hospital, and brutally beats him until the hero gets the upper hand. Once he gets the Goblin on the ground, Peter learns his true identity as he takes off his mask to reveal Norman Osborn.
Norman attempts to distract Peter so he could impale him with his glider, but his Spider-sense allows him to leap out of the way, causing Norman to be impaled by the glider and killed. Peter takes Norman's body back to his house, but is spotted by Harry, who believes that Spider-Man killed his father.
After Spidey flees, the Osborn butler Bernard cleans Norman's wounds and confirms that Norman did die by his own glider. However, to save Harry further emotional distraught, he decides not to tell him. A few days later at Norman's funeral, Harry vows that Spider-Man would pay for Norman's death. Peter visits Ben's grave and is comforted by Mary Jane, who admits her feelings for Peter and kisses him.
Unfortunately Peter denies her advances, not wanting her to be caught up in his dangerous life as Spider-Man. However, unbeknownst to Peter, MJ recognizes the kiss she had with Peter and compares it to the one she had with Spider-Man. This sparks suspicions of Peter being Spider-Man.
2003
Matt Murdock, now the vigilante Daredevil as well as a district attorney, kills a man named Jose Quesada after WIlson Fisk, now the Kingpin of crime, had financed a high paying lawyer to defend him. Ben Urich, a reporter who had been tracking Daredevil for some time, is present with the police when they find the body.
Later, while having a meetup with his business partner and college friend Foggy Nelson, Matt notices a woman enter the restaurant they were in and is immediately smitten. He asks for her name, but when he follows her after she refuses to tell him, she attacks him. Matt is able to pretty easily keep up with her, but she ultimately managed to beat him. Luckily she was impressed by Matt's skill, and gives her name: Elektra Natchios.
The two take a stroll together soon after and talk, Matt learning that Elektra's father Nikolas, a Greek diplomat, had had her train with several senseis since the age of 5. However, at the same time, Wilson FIsk hires the assassin Bullseye to kill Nikolas, as he had wanted to end his and Fisk's partnership. Daredevil attempts to stop him, but is unsuccessful and Bullseye pins him for the murder, using his baton to impale Natchios.
Afterwards, Ben Ulrich manages to deduce Daredevil's identity when he sees that Matt Murdock disguised the baton as his walking cane. Believing Daredevil to have killed her father, Elektra tries to take revenge by killing him. As they fought, Bullseye was assigned by FIsk to kill Elektra. As said person stabs Daredevil through the shoulder, he insists that he didn't kill her father.
Elektra doesn't believe him until she rips off his mask and realizes that he was Matt. moments later, Bullseye tracks down Elektra, and Matt is forced to watch helplessly as Bullseye kills her. Wounded, Matt flees to The Church Of The Holy Innocents, but Bullseye ambushes him by exploiting his weakness to loud sounds. As the police swarm the church, Bullseye reveals to Matt that Kingpin had killed his father.
Eventually an NYPD officer shoots Bullseye through both hands, allowing Matt to gain the upper hand and throw him from the belltower. Afterwards, he ambushed Fisk in his office, determined to avenge Elektra. During this fight, Fisk tells Murdock that he was ordered by Fallon to kill his father, and Elektra was nothing more than a casualty. Matt is eventually able to see Fisk after his face is drenched in rain from a broken window and defeats him.
As the police arrive to arrest Fisk, he threatens to tell the world Daredevil's identity, but he simply tells him that no one would believe Daredevil was a blind man. As this had been happening, a blind martial arts master named Stick had discovered Elektra's body and resurrected her using the ancient art of Kimagure.
After leaving her necklace with her name engraved on it with Braille on the rooftop where she and Matt first kissed, Elektra leaves to train under Stick. Matt discovers this necklace a few days later, and a day after that, Ben Urich prepares to publish an article revealing Daredevil's identity. However, he ultimately decides against this, realizing what good Daredevil had done for the city.
Meanwhile, Elektra begins training under Stick, but is expelled after only a few months because of her inability to let go of her rage and fear of seeing her mother's killer as a child. She ends up using Stick's teachings to become a contract killer for the next 2 years.
Author's note: Ok, this is going to take way longer than I thought. So many events are going to be squished into one year that you guys should expect the next 2 chapters to only cover one year. Apologies for the inconvenience and how long this took.