The Civil War was a Marvel Comics crossover event, and features the storyline of a war between superheroes.
The Superhuman Registration Act had been a long time in the making. The logical extension of the often-proposed, never-passed Mutant Registration Act, the Superhuman Registration Act arose following the devastating attack on Manhattan in reprisal for Nick Fury's "Secret War" and the Hulk's destructive rampage in Las Vegas, which killed 26 adults and 2 children (unbeknownst to the general public, The Illuminati subsequently deceived the Hulk and jettisoned him into space following this incident. See Planet Hulk). Following M-Day, 90% of the Earth's mutant population found itself spontaneously depowered. With the mutant population suddenly far less visible and extremist groups claiming the event marked a turn in the tide of growing mutants (if not divine punishment against all mutants), sympathy for the group was near an all-time low. The majority of the remaining mutants — estimated at 198—were gathered up and forced to relocate to the Xavier Institute for their own protection. These events put public support for the registration bill at around 50%.
Tony Stark (Iron Man) was among those working to prevent passage of the act. He even hired a new Titanium Man to attack him immediately after his testimony before the Commission on Superhuman Activities, hoping it would hammer home that the act would make the nation less capable of dealing with rogue or foreign superhuman threats. The anti-registration camp seemed to be making headway, and might have even defeated the bill by the narrowest of margins, if not for the events that took place in Stamford, Connecticut. Villains Nitro, Cobalt Man, Speedfreak, and Coldheart had been holed up in a house in Stamford when the New Warriors members Night Thrasher, Speedball, Namorita, and Microbe located them. The New Warriors were at the time the focus of a reality TV show, and although a number of them felt the villains were out of their league, the network and others in the group thought it would be great for ratings. When Namorita attempted to capture Nitro, he used his explosive powers and destroyed several city blocks, including the elementary school at the epicenter. Three of the New Warriors, the three villains accompanying Nitro, and over 600 civilians, among them 60 children, were killed. Numerous members of the superhero community arrived on the scene to search for survivors.
Public sentiment towards superheroes plummeted. The inactive New Warriors were widely regarded as "baby killers" by association. Hindsight Lad, desperate to distance himself from them, began releasing their secret identities until other heroes stopped him. The Human Torch is beaten into a coma outside a Manhattan nightclub. Public opinion had been lukewarm for the Superhuman Registration Act before; now it passed the tipping point. Although nominally a U.N. agency, S.H.I.E.L.D. seemed to have assumed the brunt of enforcing the act under acting director Maria Hill, even though the act was not yet passed by the U.S. Government. Captain America balks at leading a force to apprehend rogue heroes. He escapes S.H.I.E.L.D. Helicarrier when they attempt to arrest him. He begins an underground resistance movement the press dubs the "Secret Avengers". Most of his core group (Captain America, Hercules, Bill Foster, Luke Cage, Iron Fist (posing as Daredevil), Falcon, and Cable) had to take on a series of identities to avoid capture, literally becoming outlaws. The Secret Avengers apprehend a number of criminals while evading the opposing heroes and the new S.H.I.E.L.D. "capekiller" units. Other heroes join them or were liberated after their arrests. The Young Avengers, and Cloak and Dagger were some of these later heroes to join the group. Iron Man feels that it is reasonable that heroes have proper training and oversight, that the casual self-policing the superhero community had enjoyed until now was insufficient, and most importantly that it was now impossible to resist this change in the political landscape. He gathered his own pro-registration heroes to bring in Captain America's group and other non-registered combatants. Mister Fantastic, with the help of Yellowjacket and Tony Stark, began work on designing a prison named 42 to detain superpowered violators (designated 42 because it was their 42nd idea for improving the world).
Most of the pro-registration heroes, such as Mister Fantastic, Doc Samson, She-Hulk, Ms. Marvel, and Wonder Man, already had highly public identities. Even Stark unmasked himself as Iron Man (for the second time in his career), and admitted to previous attempts to hide his identity. One supporter, however, was not yet public: Spider-Man was reluctant to reveal his identity. He prepared to liquidate his assets and flee the country with his wife and aunt to avoid revealing his identity and putting them in jeopardy. They, on the other hand, were supportive and felt it was time for Peter to finally get some recognition for his good work. During a live, nationally televised broadcast, he pulled off his mask and announced, "My name is Peter Parker, and I've been Spider-Man since I was fifteen years old."
The X-Men, on behalf of the mutant community, declared neutrality in the growing conflict. Acting leader Cyclops felt that the mutants had already been through too much during the Decimation to take a stand either way and survive. Individuals within the X-Men had their own opinions on the matter, however. Wolverine felt that the act was every bit as racist and oppressive as the Mutant Registration Act, while Bishop felt it was necessary to embrace the act and make sure that mutants could continue to self-police, lest the truly oppressive regime of his home timeline should come to pass. As the last known mutants, all members of the 198 and X-Men were already in government databases and were registered by default when the act passed.
The 198 have since chafed at the constant O*N*E* surveillance, as well as their inability to leave the school grounds without being tracked by monitoring chips. When it was discovered the chips could also deliver a powerful electric discharge to assure the 198 could be subdued, they rioted. Mister M used his powers to remove the chips and they left the mansion. Bishop, Sabra, and Micromax were given permission to apprehend them, threatening to shatter Cyclops' neutrality. During the incident, General Lazer's thinly veiled anti-mutant sentiments and his covert attempts to destroy them were uncovered. His neck was snapped by Johnny Dee (via his duplicate of the general) and the mutants and heroes rallied together to prevent disaster. The more sympathetic director of O*N*E, Valerie Cooper, now seems to have a free hand with regards to the mutant refugees.
The X-Men and the 198 were not the only voices of the mutant community, however. X-Factor Investigations, an independent group of private investigators made up in part by members of the old superteam X-Factor, have recently set up shop in Mutant Town. After several incidents X-Factor has publicly and violently declared that Mutant Town is under their protection. Meanwhile, Wolverine had begun tracking down Nitro the moment rescue efforts ceased. With interference and assistance of Atlantean forces, Wolverine determines that the disaster relief company Damage Control was corrupt at the top. Nitro had been given 'Mutant Growth Hormone' to make his explosions more powerful and thus more profitable for the company. Wolverine leaves Nitro to the Atlanteans and seemingly kills the corrupt director of Damage Control, Walter Declun.
The government sets up a new version of the Thunderbolts to parry various threats, such as the plans of rogue, uncontrollable villains. The captured villains willing to play along quickly swell the team into three large squads. Still more are being trained every day in a secret mountain camp. Numerous other villains have been released since then under more direct (or less legitimate) government supervision, including the Green Goblin, the Vulture, the Jester, and Jack O'Lantern. The villains are supposedly kept in check by nanites in their blood stream which can monitor and disable them at any time. Norman Osborn, however, has learned the secret to deactivating them from a mysterious benefactor.
Most villains sought to bypass the act. Former Maggia member Hammerhead saw the act as an opportunity to usurp Wilson Fisk as the Kingpin of Crime by rallying criminals in opposition of the act. His reasoning was that it was only a matter of time before every super-being was treated as a walking WMD, and then the criminals among them were as good as dead. A number of super-criminals did in fact rally under him, but the Kingpin manages to orchestrate the capture and death of his rival from his jail cell.
Conflict among the heroes was constant, with the government-backed heroes tracking down unregistered superhumans (and subsequently arresting or registering them) and trying to find Captain America's Secret Avengers. The Secret Avengers operated out of a series of secret safehouses set up by Nick Fury, kept secret from everyone within S.H.I.E.L.D. Cap's team continued to apprehend supervillains (usually leaving them bound for the authorities), and launches a series of well-coordinated attacks on prison transports carrying unregistered superhumans. During one such raid, the convoy was diverted when Iron Man became aware of Cap's plan, and ended up going directly down Yancy Street. During the subsequent battle, a member of The Thing's beloved Yancy Street Gang dies. Ben leaves the country for a while. In Los Angeles, the Runaways, unaware of the situation, stop the Flag-Smasher in public - S.H.I.E.L.D. attempts to chase them out while severely damaging Victor Mancha, although the Runaways make it back to their lair beneath the La Brea Tar Pits. In New York, the Young Avengers see the fight on TV and the Vision II suffers a seizure. Despite Captain America's veto of the plan, the Young Avengers steal a Quinjet and track down the Runaways. After a brief fight, the two teams are attacked by Noh-Varr, who was sent by S.H.I.E.L.D. to take them down. Noh-Varr breaks Xavin's neck and kidnaps Hulkling, Wiccan, and Karolina taking them back to his prison in the Cube. During the fight, Vision II phase-shifted his hand into Noh-Varr's chest, who broke it off to escape. The remaining members of both teams break into the Cube and saved their teammates, freeing Noh-Varr from the mind control of the Cube's warden. The Runaways refuse to pick a side in the war and maintain a neutral stance.
The Secret Avengers are lured by a false emergency call into an ambush by the pro-registration forces. A clone of Thor is sent in to help arrest the fugitives, instead it kills Bill Foster. The clone then turns on the team but they are saved from certain death by the Invisible Woman. Captain America orders a hasty retreat. The event shook up both sides in the war, with Stature and Nighthawk finally surrendering and registering, while the Human Torch and Invisible Woman decide to oppose the act's enforcement with Captain America. Spider-Man decides to quit after learning about the Negative Zone prison and about spying programs on his new technological suit. He battles Iron Man and escapes into the sewers. Already weak, he was found, drugged, and blasted half to death by Jack O'Lantern and the Jester. He was saved at the last minute by the Punisher, who kills the villains and brings him to Captain America's hideout. The resistance movement is hesitant, but agree to take on the Punisher's support. Later, Spider-Man would interrupt a newscast to make a public statement about the horrors of the act's enforcement, and pledge to fight it.
Subsequently, an ambassador from the kingdom of Atlantis, on a mission of peace backed by the European Community (represented at the event by the Super Heroes of Europe), was the target of an unsuccessful assassination attempt. Norman Osborn, bearing an obviously fake press pass and handgun (and none of his Green Goblin paraphernalia), fires once at the statesman, hitting him in the shoulder. The ambassador was escorted back to the ocean by his people, and Osborn immediately collapses to the ground, claiming he was framed. Police later recognized that an accomplished menace like Osborn could have easily killed the ambassador, and that the events leading up to the shooting just didn't make sense. Osborn attempted to tell police that his actions were being controlled by a third party through the nanites, but was unable to. He was turned over to the federal government before the NYPD could learn much. Following the attack, Atlantis has massed their troops and vessels along the U.S.' east coast, as if preparing to attack (though they have not yet done so).
Public interest peaked when Speedball was found alive, hurled a state away by the force of the Stamford blast. Robbie seemed to have lost his powers in the blast (the explanation being that his powers protected him from the sudden force, but burned out their biological mechanisms in the process). Despite the legal efforts of She-Hulk, who encourages him to register, he is sent to prison, where his powers return briefly. Robbie is later shot while traveling to testify at Congress. He survives the injury but his powers kill two paramedics and injure She-Hulk. At another prison, his fluctuating powers stop a prison riot.
Trying to navigate this entire affair are reporters Sally Floyd and Ben Urich. Sally interviews both sides but ends up confused as ever. Ben Urich begins tying together events of the Civil War, from Robbie to Norman Osborn's shooting.
As the Punisher works his way through the Baxter Building to retrieve plans for File 42, Sue Richards goes to Atlantis to persuade Namor to join the Secret Avengers, but to no avail. The supervillains Goldbug and Plunderer arrive at the Secret Avengers' base to join Captain America's team, but the Punisher immediately kills them, calling them killers and thieves. Captain America attacks him and kicks him off the group, but the Punisher doesn't raise a finger against him. The Secret Avengers, joined by Storm and the Black Panther, reach the Ryker's Island penitentiary and head through the portal to the 42 complex, but the team is confronted by the pro-registration supporters, revealing that each team had placed a spy on the other. Hulkling is able to release the incarcerated heroes from the cells of the 42 complex in the guise of Henry Pym, making the odds more even.
Cloak moves the battle to the center of New York City. Namor and an army of Atlanteans join the battle alongside the Secret Avengers, followed by the Thor clone and Captain Marvel on the pro-registration side. Vision II disrupts Iron Man's armor and Captain America is able to subdue him. On the battlefield, Mister Fantastic is shot while trying to save the Invisible Woman from the Taskmaster, who is in turn pulverized by one of Sue's invisible fields, and Hercules crushes the skull of the Thor clone. As the battle rages on, the city is badly damaged. The Thing shows up in order to protect citizens from harm. Captain America's side seems victorious as Iron Man lies on the ground waiting for Cap's finishing blow. Just before Cap can hit Iron Man, several standard cops, EMTs, and firefighters hold him back, and Cap realizes how much damage the fighting has caused to the general population that they all want to protect. Wishing to avert any more unnecessary bloodshed, Cap surrenders and the team follows suit. Many of the Secret Avengers are given amnesty by the government, while Captain America is placed in jail.
Two weeks later, the Fifty State Initiative is launched and the Mighty Avengers assemble as a team. Tony Stark is appointed Director of S.H.I.E.L.D., while Maria Hill is demoted to deputy status. Some heroes move to Canada, while some stay underground, such as the New Avengers (Luke Cage as leader, Iron Fist, Wolverine, Spider-Man, Spider Woman, Dr. Strange, and Ronin). In front of his New Avengers teammates Luke Cage and Doctor Strange, Spider-Man sorrowfully dons his black costume after Aunt May is critically injured by a sniper, later revealed to have been hired by the Kingpin in response to the unveiling of his identity. At the end of the series, Tony Stark tells Miriam Sharpe "the best is yet to come sweetheart...That's a promise".
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