After a brutal battle, Bill Foster – the anti-registration hero known as Goliath - has been killed. Other members of Captain America's resistance have been captured and brought to the pro-registration faction's holding facility in the Negative Zone. Both sides have retreated in order to regroup and plan their next move.

Many heroes have been left injured, discouraged and questioning where they stand. While some of Captain America's allies have joined with Tony Stark, Spider-Man has left the pro-registration side. Jack O'Lantern and the Jester – members of a newer and more vicious Thunderbolts team – were sent to track down Spider-Man. After nearly killing him, the villains are gunned down by the Punisher, who took Spider-Man's battered body back to one of Captain America's safehouses. The resistance now has Frank Castle on their side.

ACT 1: At a S.H.I.E.L.D. base in Arizona, Commander Maria Hill and Hank Pym (a.k.a. Yellowjacket) are watching super-heroes train to become part of a new super group called the Champions, which will be based out of California, as part of the Fifty State Initiative. Other groups are also being formed, as revealed by Commander Hill, and they consists of the Mormon heroes in Utah, the Spaceknights in Chicago, and – pending background checks and final approval from the local authorities – Force Works in Iowa. Their conversation is cut short by the appearance of a S.H.I.E.L.D. agent informing Hank that they are having some kind of problem with the super-powered individual known as Poseidon. Excusing himself to Commander Hill, Hank follows the agent.

ACT 2: Meanwhile, at the Baxter Building, Reed Richards is performing brain surgery on the Thor clone, trusting that the implant he is putting in his head will stop him from killing anyone during the final battle. While doing so, he is on the speakerphone with Iron Man, who is relaying information about the situation on the ground. Iron Man explains that crime is at an all-time low and comments that it will be quite boring for the new heroes once they are up and running. Reed replies that boring is a good thing, and means that little kids are not going to get buildings pushed on top of them, obviously alluding to the Samford tragedy. Tony asks Reed how his meeting with the President went. Reed explains that he read him the Riot Act and told him that he would not take part in the final battle unless he has an absolute guarantee that his wife, Sue, and brother-in-law, Johnny, are given full pardon. Tony asks if the President agreed to his proposition and Reed replies that the President agreed to let them choose twelve super-powered individuals to be immune from prosecution; but everyone else would be prosecuted to the full extent of the law. Tony replies that he will take care of the rest as he is seeing the President for dinner anyway.

ACT 3: In another part of the building, unbeknownst to Reed Richards, the Punisher is making his way through the ventilation system undetected thanks to a special suit that has cloaking dampers. As he proceeds through various levels, he is in constant communication with Captain America, who oversees the break-in operation from the secret Avengers headquarters. The Punisher reaches the Baxter Building's data-house and starts to download information about the Number 42 prison complex located in the Negative Zone. The Punisher comments that it is going to be difficult to break in there because it is heavily protected.

ACT 4: While the break-in takes place, the Invisible Woman heads to Atlantis to try and convince Namor to join the anti-registration side, as they could greatly use his help. Namor, however, rejects her proposition, claiming that Captain America used her by sending her to enlist him because of their "unique" relationship. Sue argues that they do not have a relationship but Namor believes Sue still has feelings for him.

ACT 5: A short time later, at the anti-registration camp, the Punisher has returned from his mission so the heroes gather together to discuss their plan of attack of the Negative Zone prison. Falcon explains the pro-registration plan to have puppet heroes in every state with fifty portals leading directly from their local penitentiary into the Negative Zone prison. Two of the portals have already been completed and they – meaning the anti-registration team – have obtained the codes for the one on Ryker's Island. Captain America goes on explaining that they need to move fast because, according to his sources, the pro-registration team, along with the new Thunderbolts and S.H.I.E.L.D., are planning a huge assault. That night is therefore their absolute last opportunity to make their move. Captain America then turns to Spider-Man and tells him that they will understand if he sits this one out, as he is still not in the best of shape, since the beating he received at the hands of the Jack O'Lantern and the Jester. Spider-Man replies that there is no way in hell that he is sitting this one out and comments that they are already outnumbered enough as it is. With that said, the hero known as Diamondback speaks up and tells them the numbers are not that bad. As she says that, the villains known as Goldbug and Plunderer step out of the shadows to offer their services to Captain America's anti-registration team. Seeing as Iron Man already has villains working for him, they thought Captain America could use them to level the playing field. Before Captain America can answer, the Punisher shows up and riddles the two villains with bullets, seemingly killing them. Totally infuriated, Captain America punches the Punisher, calling him a "murderous piece of trash". The Punisher argues that they were bad guys but Cap kicks him in the face and tells him to shut up. He then slams his shield hard on him while busting his jaw with his knee. The Punisher is then slammed into a wall where Cap calls him a coward and tells him to fight. The Punisher replies that he will not fight back so Captain America lets go of him and tells the others to take him out of there. Witnessing this, the hero known as Patriot asks Spider-Man if he knows why the Punisher would not hit Captain America. Spidey replies that Captain America is probably the reason the Punisher went to Vietnam. "Same guy, different war" he adds. Captain America turns over to them and tells Spidey he is wrong because the Punisher is insane and he is not, though one might argue.

ACT 6: Meanwhile, in Stamford Connecticut, Iron Man and Reed Richards meet with Miriam Sharpe, the mother of one of the children that was killed in the blast, at the site of a memorial in the children's honor. Miriam thanks them for all that they have done to avenge the death of her son and the other kids, despite what it personally cost them. Tony replies that there is no shame in making enemies if it means making people safer.

ACT 7: At the North Pole, home of Dr. Strange's sanctuary, Uatu the Watcher visits Dr. Strange and asks him why he has not try to end the war using his mystical powers. Dr. Strange replies that there is no right or wrong in the debate and that it is not his place to interfere with the evolution of the superhuman role. Uatu replies that he is familiar with such dilemmas but asks Dr. Strange why he is fasting if he favors no side and what outcome he is meditating for. Dr. Strange replies that he is meditating for whichever victory is best for all mankind and spills the least amount of blood.

ACT 8: That night, at Ryker's Island Penitentiary, the anti-registration team, which consists of Captain America, Spider-Man, Hercules, the Human Torch, Vision, Storm of the X-Men, Spider-Woman, Black Panther, Tigra, Falcon, Luke Cage, Patriot, the Invisible Woman, to name a few, makes its move and, after disarming the security team guarding the portal to the Negative Zone, use said portal to access the Number 42 prison complex. But as they enter the heavily secure complex, Spider-Man's spider-sense kicks in, warning him of danger. Just then, a large door slides open, revealing Iron Man and his team of pro-registration heroes and villains (namely the new Thunderbolts). Arrogant as usual, Iron Man tells Captain America that he fell right into his trap, thanks to a mole inside Cap's organization, and that he is outnumbered ten to one, so he and his team should surrender. Cap replies that they knew about Tigra being the mole and tells Iron Man that he too has a spy in his team. Iron Man replies that it is impossible because the only people who knew about Tigra were himself, Reed and Hank Pym. As he says that, Hank Pym steps forward, removes his mask and transforms into Hulkling the shape-shifting Young Avengers (Hulkling revealed that he abducted and drugged Hank earlier that day when he impersonated the S.H.I.E.L.D. agent who needed help with Poseidon). When Reed Richards realizes that Hulkling was able to mimic Hank's voice and retinal pattern and therefore had full authority to do whatever he and Tony can do, he starts to freak out. Tony also comes to the realization of what that implies, just as all the heroes that were imprisoned in the Negative Zone prison arrive to fight on Captain America's side. The issue ends with the promise of a full-scale battle between Captain America's anti-registration team and Iron Man’s pro-registration group.

To be continued in Civil War #7.