At the start of this issue, Spider-Man is swinging through the city when he hears someone screaming in fear. He heads to where the screaming is coming from to find a group of people in masks kidnapping a young woman. As he fights the thugs and gets rid of them one by one, someone on a rooftop opposite the alley Spider-Man is in aims a rifle towards the street, and fires a shot when the scope is aimed at Spider-Man. The shot misses Spider-Man and hits a fourth thug who was sneaking up behind him. Spider-Man muses that he has a guardian angel, and then looks to where the bullet should have come from, to see that no one is there. The girl who was being kidnapped goes to thank Spider-Man, but collapses from the fear and shock. An ambulance and some police cars arrive shortly afterwards, and Spider-Man takes the girl to the ambulance, but swings off when the police ask him to answer some questions.
The Punisher is driving his war wagon shortly afterwards, and fills out a war journal entry. In it, he says that he encountered the enemy today, and that he saved Spider-Man from being killed by the enemy (which explains who fired the shot). He adds that he was unable to question the men who attempted the kidnapping due to the police's presence. The Punisher then heads to his base, an abandoned power station, and is surprised to find that Spider-Man has stowed away in his van. Spider-Man has worked out that it was the Punisher who fired the shot that saved his life, and questions the Punisher about it. The Punisher replies that he had received a tip that the group was going to perform a kidnapping that night, and had been planning on following them until Spider-Man intervened.
Spider-Man asks why the Punisher had been concentrating on that particular group, and the Punisher shows Spider-Man a canister of biochemical toxic gas, which Spider-Man assumes is government property. The Punisher corrects him, saying that the gas is for sale to anyone who can afford the price. He then shows Spider-Man footage of the same gas being tested on people in an as-of-yet unidentified country, which kills them horrifically. The Punisher explains that the girl Spider-Man saved was going to be kidnapped and have more deadly weapons tested on her, along with whoever else was kidnapped in the process. Spider-Man gets annoyed with the Punisher for planning on just letting innocents be captured and having deadly weapons tested on them for his sake, and starts attacking the Punisher. The Punisher retaliates by shooting Spider-Man with a drugged dart.
Later, the Punisher fills out another war journal entry, saying that he's found the leader of the kidnappers, a man named Moses Magnum, at the offices of the Deterrence Research Corporation. He adds that Spider-Man recovered from the dart and has agreed to help him in his mission, then starts his assault on the building, leaping through a window in the hope of catching the enemy guards by surprise. The Punisher is successful in killing the guards on the ground floor, and disables the building's alarm system before entering the stairs and going higher in the building. Spider-Man, meanwhile, is climbing along the outside of the building when a homing device the Punisher gave him starts beeping, signalling that he's on the same floor as Moses Magnum. He then uses a glass cutter the Punisher gave him to get inside the building, and takes out some guards in the darkness of the building before heading for an office where he finds Moses Magnum. Magnum immediately orders his guards to kill Spider-Man.
Whilst this is happening, the Punisher reaches the building's private power plant, and is able to take out most of the guards in the plant before before being ambushed from behind. Although it seems as if the guard who is crushing him from behind is going to stop the Punisher, the Punisher manages to run the guard into a wall, which knocks him out. Back in Magnum's office, Spider-Man is being defeated by guards when Magnum changes his mind and orders his guards not to kill Spider-Man after all, as he is more useful alive. Spider-Man is defeated just as the building's power is cut by the Punisher. Magnum then takes Spider-Man and his guards into his private hover-copter, and flies away. From the ground level of the building, the Punisher watches the copter get away, and thinks to himself that everything is happening according to plan.
Much later, Spider-Man is kicked out of the hover-copter into an area surrounded by guards and barbed wire fences, where he finds several other people who have been kidnapped and taken there. As Spider-Man tells them how he came to be there, a guard arrives and tells Spider-Man that Magnum wants to see him. Spider-Man starts attacking the guard at first, until another guard threatens to kill some of the people there unless he comes to see Magnum. Upon reaching Magnum, Spider-Man purposely annoys Magnum, who pulls Spider-Man's mask off. Underneath, however, isn't Peter Parker's face but a strangers. Magnum says that he's going to kill Spider-Man before searching the records of major companies in Manhattan, to find out who he was. Spider-Man keeps being his flippant self, until Magnum punches him in the gut and orders his guards to take him away.
Once alone, Spider-Man takes out some plastic moldings which the Punisher gave him and straightens his hair, revealing himself to be Peter Parker after all, just with a disguise on. Later that night, the Punisher manages to break into the hut which Spider-Man is in thanks to a homing device which was sewn into Spider-Man's costume, and gives Spider-Man a gas mask, since he's brought some gas bombs to use. The Punisher also tells Spider-Man that he did some research on Magnum, and found out that he was born in Ethiopia prior to Mussolini's invasion, and joined Mussolini against his own people when Mussolini invaded. The Punisher and Spider-Man then start sneaking around the base, taking out guards where they can, but before long the alarm is sounded.
The Punisher and Spider-Man seem outnumbered, but thanks to the gas bombs which the Punisher brought, most of them are easily defeated. Spider-Man breaks into Magnum's fortress, and finds Magnum alone. However, he's surprised to find that Magnum is stronger than he seems, as well as having greater fighting skills, almost breaking Spider-Man's back. Magnum manages to grab a canister of the gas which he was testing on the people his men kidnapped, and raises it above his head, about to throw it down onto Spider-Man. The Punisher then enters, and shoots the gas canister, despite Spider-Man telling him not to. Spider-Man rushes out of the room with the Punisher, and they manage to close the door just before the gas escapes the room.
The Punisher then fills out a war journal entry, saying that Moses Magnum has certainly been defeated by the dissolving gas. He and Spider-Man manage to contact the local authorities, as well as the United Nations, who arrange for transportation back for the kidnapped victims. Spider-Man says that he's going with them, unlike the Punisher, who has his own transportation out of there. Before they go, Spider-Man asks the Punisher whether he heard his warning about Magnum's gas and not to shoot it. The Punisher replies "Of course". Spider-Man then asks why the Punisher shot it, before deciding that he doesn't want an answer.
This issue also reprints The Amazing Spider-Man Annual #2 story "The Wondrous World Of Dr. Strange!"