Appearing in 1st story
- Initiative (First appearance)
- Cap's Secret Avengers
- Human Torch (Johnny Storm)
- Invisible Woman (Sue Storm)
- Spider-Man (Peter Parker) (Joins team)
- Punisher (Frank Castle) (Joins team)
- Tigra (Greer Grant)
- Black Mamba (Tanya Sealy)
- Living Lightning (Miguel Santos)
- Daredevil (Danny Rand)
- Diamondback (Rachel Leighton)
- Ultra-Girl (Suzy Sherman)
- Monica Rambeau
- Young Avengers
- Falcon (Sam Wilson)
- Firebird (Bonita Juarez)
- Justice (Vance Astro)
- Luke Cage
- Machine Man (Aaron Stack)
- Stingray (Walter Newell)
- Dr. Jane Foster
- Misty Knight
- Night Nurse (Linda Carter)
- Triathlon (Delroy Garrett Jr.)
- Venom (Mac Gargan)
- Bullseye (Lester)
- Radioactive Man (Chen Lu)
- Songbird (Melissa Gold)
- Jester (Jody Putt) (Death)
- Taskmaster (Tony Masters)
- Atlas (Erik Josten)
- Vector (Simon Utrecht)
- X-Ray (James Darnell)
- Lady Deathstrike (Yuriko Oyama)
- Jack O'Lantern (Steven Levins) (Death)
- Joystick (Janice Yanizeski)
- Ironclad (Michael Steel)
Races and Species:
- Human-Olympian Hybrids
- Human-Kree Hybrids
- Skrull-Kree Hybrids
- New York State
- Negative Zone
- Captain America's Shield
- Captain America's Uniform
- Extremis Armor
- Iron Spider Armor (Destroyed)
- Patriot's Uniform
- Falcon's Wings
- Stingray's Suit
- Venom Symbiote
Synopsis for 1st story
Nighthawk and Stature join the Pro-Registration side at Stark Tower. Happy Hogan tells both of them that Tony Stark wants to welcome them personally.
Iron Man and Spider-Man square off. Iron Man tells Spider-Man that he is acting like a lunatic. Iron Man asks Spider-Man to sit down so they can talk rationally. Spider-Man says that the Negative Zone prison is insane. Iron Man says that the Negative Zone prison is only a temporary measure; that there were no normal prisons capable of holding metahumans.
Iron Man says that the government had wanted to outlaw all super heroes and that the Registration Act was a compromise. Iron Man tells Spider-Man to think about May and Mary Jane. Spider-Man then punches Iron Man through a wall. Capekillers then enter the room and blast away at Spider-Man. Iron Man yells at the capekillers to hold their fire. The bullets break open the reinforced glass windows of the building, allowing Spider-Man to escape.
Maria Hill tells Tony Stark that she is sending the Thunderbolts after Spider-Man. Iron Man pleads with Maria to just let him try and talk to Spider-Man. Maria denies Iron Man's request and sends a couple of the new Thunderbolts after Spider-Man. Maria mutters that she knew that they could not have ever trusted Spider-Man.
Spider-Man runs through the sewers. Suddenly, Spider-Man is attacked by the Jester and Jack O' Lantern. The two villains say that they may not love working for S.H.I.E.L.D., but that they do love the chance to get to beat up on Spider-Man. Jester and Jack O' Lantern lay a serious beat-down on Spider-Man. But, before they can take Spider-Man into custody, a bullet blast opens Jack O' Lantern's head and another bullet blasts apart the Jester's head. The Punisher is on the scene to rescue Spider-Man.
Invisible Woman and Human Torch use their new disguises given to them by Nick Fury. However, they have to pose as husband and wife. They enter Captain America's new headquarters. The Anti-Registration heroes are all meeting. They are discussing how Cloak and Dagger got caught by the Pro-Registration side. Captain America is angry that for every person they gain, they seem to lose one to the capekillers. Suddenly, Punisher walks into the room and demands medical attention for a badly beaten Spider-Man.
Spider-Man is taken to the Infirmary. Meanwhile, the Falcon asks Punisher which side he is on. The Punisher responds that since now the Pro-Registration side is enlisting the aid of known thieves and killers, he is now on the Anti-Registration side. The various members of Captain America's team do not want Punisher with them as they do not want to be so far gone that they are signing up with people like the Punisher. Captain America tells everyone to be quiet while he thinks about whether or not to let the Punisher join them. Tigra, hiding in the shadows, calls Tony on her cell phone.
A squad of capekillers place Daredevil into custody. Reed Richards and She-Hulk are on the scene. Reed mentions how the public is behind the Pro-Registration side and so is the U.S. government; that crime is at an all time low; and that the only people causing problems are other super heroes in the Anti-Registration side. Reed laments that he wishes he never got involved; that he is sick that they are using the criminal lunatics in the Thunderbolts; that Hank Pym is doped up on anti-depressants. She-Hulk responds that public opinion would have forced S.H.I.E.L.D. to bring down every single super hero in America; that the public was sick of sixteen-year-old kids blowing up buildings; that Reed and Tony Stark gave everyone a future.
Tony Stark accompanies Daredevil to the Negative Zone prison. Tony tells Daredevil that he hates hunting down his friends, but there was no other option as the U.S. government was going to institute a complete ban on all super heroes and this Registration Act was the only other option.
Tony tells Daredevil of their plans for fifty super teams spread over all fifty states. Each one license and accountable to the taxpayer. It is the next stage of superhuman evolution: a Federal force from coast to coast. Tony asks Daredevil to join him and to lead one of these fifty teams. One of the guards tells Tony that they found a silver dollar under Daredevil's tongue and gives it to Tony. Daredevil comments that Tony now has thirty-one pieces of silver. Daredevil then says, "Sleep well, Judas."
- Stature and Nighthawk officially join the pro-registration side.
- Spider-Man leaves the pro-registration side.
- Cloak and Dagger are revealed to have been captured.
- Daredevil is captured and escorted to Prison 42 by Tony Stark.
- The cover date and release date are both November 2006, reflecting the production delays that Marvel experienced during the Civil War event.