“They’re right. We’re not fighting for the people anymore, Falcon… Look at us. We’re just fighting.” – Steven Rogers
In a battle between Nitro and the New Warriors, Nitro explodes which seemingly kills the entire team and a large number of civilians, which leads to the government introducing the Superhuman Registration Act and sparking a Civil War between the superhuman communities. The Act had been a long time in the making and arose following the devastating attack on Manhattan during Nick Fury’s Secret War as well as Hulk’s rampage in Las Vegas which killed 26 adults and 2 children. After M-Day when 90% of the Earth’s mutant population was de-powered, the remaining 198 were gathered and forced to relocate to the Xavier Institute for their own protection and Tony Stark was originally among those to prevent passage of the Act. Later, Nitro, Cobalt Man, Speedfreak and Coldheart were lying low in a house in Stamford, Connecticut when the New Warriors tracked them down while filming a reality TV show. Although most of the team thought these villains were out of their league without Nova, Speedball thought otherwise so they began their raid and when Namorita attempted to capture Nitro, he used his ability to explode and destroyed several city blocks, killing the team, other villains and 600 hundred civilains (to include 60 children). Shortly after, numerous members of the superhero community arrived to search for survivors while public sentiment suddenly plummeted towards superheroes. The inactive members of the New Warriors are then widely regarded as baby killers by association so Hindsight begins releasing the team’s secret identities in order to distance himself, but many of the members are soon killed by lynching.
Outside a Manhattan nightclub, the Human Torch is also beaten into a coma as the Superhuman Registration Act is officially passed with S.H.I.E.L.D. gaining the brunt of enforcing the act under Director Maria Hill. Captain America hesitates on leading a force to apprehend rogue heroes, feeling heroes should be above direct government control in order to prevent politicians from controlling heroes so he escapes the Helicarrier and begins organizing other anti-registration heroes into a group dubbed the Secret Avengers. Most of his core group had to take a series of identities to avoid capture and become outlaws while also apprehending a number of criminals while also evading capture. Iron Man however, feels the Act is reasonable and heroes should have proper training, and the self-policing of the superhero community was becoming insufficient so he gathers his own pro-registration heroes to bring Cap and his group in. Reed Richards, Henry Pym and Stark then begin working on designing a prison in order to detain the super-powered violators in the Negative Zone, and although most of the pro-registered heroes already had highly public identities, Spider-Man was originally reluctant and even prepared to liquidate his assets and flee the country with Mary Jane and Aunt May to avoid putting them in jeopardy. Eventually, Spider-Man pulled his mask off during a nationally televised broadcast and announced his secret identity after being convinced by his wife and aunt. The X-Men declared neutrality in the growing conflict, with Cyclops feeling mutants had already been through too much during Decimation to take a stand and survive, but other X-Men had their own opinions.
Eventually the 198 were already in the government database and registered by default when the Act passed so they were left out of the conflict but kept under constant surveillance with an implanted microchip until they were removed by Mister M. Meanwhile in Mutant Town, de-powered mutants were becoming easy targets for hate groups but X-Factor Investigations set up shop in the town and informed the public that they are declaring the town off-limits via press conference after the Act passed. Meanwhile, Wolverine had begun tracking Nitro and tracked him to a cabin while S.H.I.E.L.D. also tracked the villain, but when everyone arrives; Nitro explodes and incinerates everything within a wide radius to include the S.H.I.E.L.D. agents and Wolverine is reduced to an Adamantium-plated skeleton. While regenerating, Wolverine overhears Nitro talking to a phone contact which goes south and when Howlett recovers, the two begin fighting again and Wolverine keeps within a small radius in order from being incinerated again. The fight is then interrupted by a trio of Atlanteans who are seeking to bring Nitro back to Atlantis where he is wanted by Namor for the murder of Namorita. Wolverine decides to join them on their trip to Atlantis in order to talk to Namor but before leaving, Nitro frees himself and tries to take an Atlantean woman hostage, but Wolverine subdues him and cuts his hand off in the process and leaves the villain to Atlantean justice in order to pursue the source of the Mutant Growth Hormone. Meanwhile the government recognizes the upcoming war between heroes is leaving the country defenseless against super-villains so the Thunderbolts are asked to lead Operation: Justice Like Lightning, in which they would confront, capture and reform villains.
It was unrealized that Helmut Zero had already been collecting villains to form an army to confront the Grandmaster and is Squadron Sinister and the Thunderbolts are divided into three large squads. Other villains are released, but kept in check by nanites in their blood stream which can disable them at any time, but Norman Osborn learned the secret to deactivating them. Most villains sought to bypass the Act so some of them grafted Skrull tissue into their bodies while Hammerhead saw the act as an opportunity to seize control from Wilson Fisk as the Kingpin of Crime by rallying criminals in opposition of the act. Although many criminals did ally themselves with Hammerhead, Fisk still managed to orchestrate the capture and death of his rival from his jail cell by deceiving Stark into believing they were raiding Cap’s secret base. The conflict among the heroes became constant with government-backed heroes tracking the unregistered super-humans while trying to locate the Secret Avengers who operated out of a series of secret safe houses set up by Nick Fury. Cap’s team continued to apprehend super-villains while also launching a series of well-coordinated attacks on prison transports carrying unregistered super-humans. During one of the raids on Yancy Street, the Thing was visiting his old neighborhood and was roped into crowd control, but when a young member of the Yancy Street Gang died in the riot, Grimm became so disgusted, he left the country. In Los Angeles, the Runaways stopped Flag-Smasher and were chased out by S.H.I.E.L.D. who injures Victor, while in New York; the Young Avengers witness the fight and steal a Quinjet to track the Runaways down.
After a brief fight, the two teams are attacked by Noh-Varr who was sent by S.H.I.E.L.D., breaking Xavin’s neck while also stealing Hulkling, Wiccan and Karolina in order to take them back to his prison in the Cube. During the fight, Vision phases his hand into Noh-Varr’s chest, but gets broken off in order to make his escape while the remaining members break into the Cube to save their teammates and free Noh-Varr from mind control. The Secret Avengers are later lured into a false emergency call which turns out to be an ambush by pro-registration forces where a clone of Thor is released and kills Bill Foster by sending a bolt of lightning through his chest. Cap then orders a retreat and both sides are shaken so Stature and Nighthawk surrender in order to register while the Human Torch and Invisible Woman decide to oppose the act and join Cap. Spider-Man then becomes curious about the details of enforcement and comes to realize Stark was using his Iron Spider suit to monitor his actions and reactions, to include his spider-sense and an added override codes to subdue Spidey if necessary. When Parker accompanied Stark on a visit to 42, he learned many of the captives were being held without trial or access to counsel so Spidey rebelled and was attacked by Iron Man when attempting to sneak away with Mary Jane and Aunt May. The three managed to escape and several registered villains were sent to capture Spidey but saved by the Punisher who then brings him to Cap and is reluctantly accepted on the anti-registration side.
Shortly after, the government tried discrediting Cable who has been opposing the act because he sees it as the first step towards government-sponsored teams, followed by a super-powered police force which will ultimately lead to a global police state. After Cable overthrows Flag-Smasher as President of Rumekistan, many in the world believed Nathan was a threat to international stability so the Six Pack was sent to discredit Cable, but the plot was halted and exposed. After an assassination attempt on an Ambassador from Atlantis failed, the kingdom mass their troops along the East Coast in preparation of an attack while the U.S. was also in the midst of a cold war with the Inhumans over their refusal to return stolen Terrigen Crystals. Public interest also peaks when Speedball is found alive after being hurled a state away by the force of the Stamford blast and seems to have lost his powers to be held without a trial, but was eventually given counsel by Jennifer Walters. Instead of registering, Speedball refused so he was put into the prison’s general populace where he was regarded as a baby killer and regularly beaten so he challenged the toughest prisoner to a boxing match where his powers kicked in. Robbie was then placed into solitary and decided to testify before Congress on the Stamford incident but was shot while being escorted to be later mended by Reed Richards and returned to prison at the Raft. While there, Robbie was taken hostage by a group of super-villains to be used as a human shield, but his powers activated once again and later registered.
Meanwhile, Frank Castle worked his way through the Baxter Building in order to retrieve plans for File 42 while Susan Storm went to Atlantis in order to persuade Namor to join the Secret Avengers, but the Sub-Mariner turned her down. Goldbug and Plunderer also arrive at the Secret Avengers’ base to join Cap’s team but Castle immediately kills them so Steve attacks him and kicks him out of the group, but Punisher refuses to fight back due to respect. Cap’s team then reach Ryker’s Island along with Storm and T’Challa and head through the portal to Prison 42, but is confronted by pro-registration forces. Hulkling manages to release incarcerated heroes and as the battle begins, Cloak moves the battle to the center of New York City, while Namor and many Atlanteans also join the fight on the side of anti-registration forces. During the battle, Iron Man’s armor is disrupted by Vision so Cap subdues him while Reed is shot on the battlefield while trying to save Sue from Taskmaster and Hercules crushes the skull of the Thor clone. As the battle rages on, the city is being destroyed and Thing returns to protect its citizens from harm. Cap’s side seems to be victorious as Iron Man waits for the finishing blow, but just before Cap hits him, several cops, EMTs and firefighters hold him back and Steve realizes how much damage the fighting has caused so in order to avert anymore unnecessary bloodshed, he surrenders. The anti-registration forces follow and many of the Secret Avengers are given amnesty by the government while Cap is placed in jail. Two weeks later, the 50-State Inititative is launched and the Might Avengers assemble while Stark is appointed Director of S.H.I.E.L.D. and Maria Hill is demoted to Deputy Director. Some heroes choose to relocate to Canada while some stay underground.