In a large mansion, somewhere in Upstate New York, a briefcase is exchanged, the content of which is apparently very deadly. The briefcase carrier, a man named Fernando, asks the recipient, Carlo, if he wishes to "test the product". Carlo’s response seems to indicate that "testing" it would be highly dangerous and likely lethal. Fernando simply wants to protect his reputation as a smuggler; he doesn't want Carlo to think he's tampered with the package. Carlo reassures Fernando that Moses Magnum designed the briefcase, meaning that, had he tampered with it, he probably would not be there to make the delivery; he would be dead. Just then, gunshots are heard in the distance. Then, before anyone can figure out what is going on, a large explosion takes out the front door and surrounding walls. Several of Fernando's and Carlo's men are killed in the blast. As the dust and debris slowly settles down, the Punisher's insignia is seen through the dense smoke. The man open fire in that direction, emptying their guns at what they believe is the Punisher. It turns out, however, that what they just shot at is some sort of police tactical robot mounted on a set of tracks, with a large skull face attached to its front. In a matter of seconds the majority of the men are slaughtered by a barrage of bullets. Still in possession of the briefcase, Carlo manages to make a run for it and escape death by throwing himself out one of the windows. Carlo lands face first into the hard ground, right at the feet of the Punisher. The Punisher tells Carlo to get back on his feet, which he does. Carlo indicates that the briefcase cannot be opened safely, as it is booby-trapped. The Punisher doesn't seem to care for such a detail and tells Carlo that the two of them will see if it is really booby-trapped. Having said that, the Punisher detonates his robot, effectively destroying the entire mansion.
The following day, we find Peter Parker driving a cab, rather poorly, through the Manhattan streets. In an effort to make additional money, Peter's decided to become a taxi driver, which he was told can make a lot of money in one day. Unfortunately for Peter, his driving abilities are no match to his web-slinging abilities and the whole cab drive ends up being a nightmare for him, and the instruction sitting in the passenger seat next to him. At the conclusion of the cab driving lesson, Peter is handed a pile of books and is asked to come back in the following Monday to take the exam again.
Walking away from the DMV office, holding onto a huge pile of book, Peter accidentally runs right into the Punisher, on his way home. Peter immediately recognizes him and uncomfortably stares at him for too long a period of time. The Punisher turns to him and asks rather loudly what he’s staring at. Embarrassed, Peter utters a weak response and the Punisher strides away. Coming back to his sense, Peter realizes that he ought to follow the Punisher to see what he is up to, especially since he's been known to kill people carelessly, guilty or not. Peter drops his book onto a nearby hotdog stand and takes off after the Punisher.
The Punisher arrives at a warehouse in Far Rockaway Queens and proceeds to watch a DVD he's obtained from an unidentified source. The DVD footage features Moses Magnum discussing a new drug of his – gamma irradiated mutant growth hormone. The footage shows Magnum injecting the drug into an unwilling human test subject and releasing him in a simulated hostile environment. Within seconds of having been injected, the drug takes effect. When approached by local villagers, where he was dropped off, the test subject reacts like a wild animal, killing all those that came to his aid, including children. Magnum sadistically comments that no actual peacekeepers were harmed in the making of the video (he had made reference to the villagers as U.N. peacekeepers at the beginning of the video, for the purpose of his drug trading scenario). Having watched the same footage from the rafters, Spider-Man is completely disgusted. Before he can do anything, the Punisher unexpectedly turns around and tosses a metal chair at him. Spidey dodges the chair, performing a series of summersaults. As he lands on a bunch of crates, he finds himself with a gun between the eyes, courtesy of the Punisher. The Punisher tells Spidey to take a hike, as this is not in his area of expertise. Spidey argues that Magnum has earthquake-making powers now, which makes him a potential villain in his wheelhouse, so to speak. The Punisher replies that he doesn't care what Magnum can do, as long as he bleeds when he gets shot. Spidey asks the Punisher if his will is to hunt down Magnum by himself, without any outside help. The Punisher replies that he doesn't need to hunt him down, as he's already tracked Magnum’s operations to the warehouse they are standing in right there and then. The Punisher is actually surprised Magnum is not there already, especially since he's halted all of his operations in North America and stolen a serum he's invested millions of dollars into. Spidey asks what the Punisher intends to do once he has Magnum. The Punisher replies that Magnum and all those involved with him in any way deserve what is coming their way, especially seeing as they've killed innocent children and entire families just so they could test their drugs. Spider-Man tells the Punisher that maybe they can get the Avengers to help them with this thing, as opposed to just killing everybody. The Punisher appears to not be listening so Spidey spins him around to talk to him. The Punisher, a large grin on his face, points to his ears and tells Spidey he's wearing earplugs. Before Spidey can do anything, the Punisher activates some kind of extremely loud alarm, which causes our hero to not be able to do anything else but plug his ear and fall to his knees in agony. His spider-sense completely useless because of the noise, Spidey is unable to react when the Punisher traps him inside a net and then knocks him out. The Punisher is in the process of attaching the trapped Spidey onto a large hanging hook when an explosion rocks part of the warehouse – Moses Magnum is home!
Magnum, surrounded by his henchmen, instructs the Punisher to give him back what's his or else. Before Magnum can carry on with his threats, the Punisher sets off more robotic weaponry that unleash a barrage of bullets and missiles, obliterating Magnum's men. Infuriated, Magnum starts using his earthquake-making powers to try and stop the Punisher. The Punisher takes off swinging on the hanging hook (with Spidey in the net) and lands next to a speedboat. He then takes one of Spidey's spider-tracers, swallows it and cuts Spidey loose into the river. He then turns to face Magnum, as the whole warehouse starts crumbling around him.
The story then cuts to J. Jonah Jameson, who's home doing yoga, looking after his plants, and trimming his moustache. A knock on the door interrupts his peaceful routine. When Jonah opens the door, the man known as the Bookie makes his way inside the apartment uninvited, accusing Jonah of being a murderer – the infamous spider-tracer killer. Surprisingly, Jonah remains calm and asks the Bookie to explain himself. The Bookie indicates that his investigation has led him to believe the killer might have a thing for justice, which is something right down Jonah's alley. Furthermore, through some of his connections with the force, he's discovered that the spider-tracer are so well-made that they actually work, which also means that someone would have had to pay top dollars to pull that off. The Bookie knows Jonah has a lot of cash, which is another reason why he thinks Jonah is the spider-tracer killer. Plus, if you add to the equation all the various attempts to capture Spider-Man that Jonah has funded, it makes even more sense that he could have funded the production of spider-tracers. Still not done with his wild accusations, the Bookie explains that the last victim, a woman named Julia Delphi, was a volunteer in Bill Hollister's campaign office, which sent Jonah a missive indicating that they were not interested in Jonah's endorsement of their candidate for mayor. The Bookie believes Jonah killed Julia Delphi in retaliation to having his endorsement rejected. Finally, Jonah gets his chance to speak. After checking his pulse to make sure he is not close to having another hear attack, Jonah explains that he spent the last four months in the hospital, recovering from an aortal rupture. While he recuperated, the doctors told him that he would have to make very profound changes in his lifestyle, to survive longer. One of the thing Jonah has been working on is how to deal with stress; he's adopted a new mantra, a phrase he repeats over and over again: "I will not die before Spider-Man". Every time he utters that sentence, the thought fills him with grace and peace. Jonah never really had the chance to test it out in the real world, until now. He is pleased to see that, if he can listen to a moron play armchair detective, which must mean it is working. He thanks the Bookie for the test and wishes him good day. The Bookie was expected a different reaction from Jonah and threatens to go to the cops with what he has. Having turned his back to the Bookie, Jonah suddenly turns around and uses a stun gun on the Bookie, sending him writhing in pain on the ground. Jonah tells the Bookie that both candidates turned down his endorsement; a classic case of covering one's political ass. He tells the Bookie to have a nice day and tosses him outside his apartment. As the Bookie lies on the ground, he realizes he’s made a big mistake; however, something Jonah said has given him a big clue as to the identity of the real spider-tracer killer.
Spidey awakens in the river, his lungs screaming for air. He quickly begins his ascension through the murky river water. Meanwhile, on a boat somewhere on the river, the Punisher is being tortured by Moses Magnum into revealing the location of the serum he stole from him. Though in pain, the Punisher keeps mum.
Having overcome drowning, Spidey lays on the docks, catching his breath. His spider-sense is still tingling; however the tingle is leaving, slowly. That's when he spots a boat a few miles down river and realizes that he needs to get to that boat, because whatever is on the boat is making his spider-sense tingle. Spidey "borrows" a speedboat from a nearby bystander and takes off after the boat.
On said boat, Moses Magnum is getting nowhere with the Punisher, who still refuses to reveal where he's hidden the gamma-irradiated serum. Though Magnum has had his men search the Punisher, they have found no trace of it. It turns out that the Punisher embedded in his flesh the tiny serum capsule, which he now pulls out, unbeknownst to Magnum.
When the boat starts to bog down, one of Magnum's men decides to go check on the engine to find out what is going on with it. As he exits the boat's command centre, he notices Spidey's empty speedboat behind them. Just as he alerts the other man at the boat's helm, Spidey crashes through a window and takes that man out. The same man, who noticed Spidey in the first place, manages to call for backup before being taken out. Spidey is then forced to battle many more of Magnum’s henchmen.
Magnum continues his beating of the Punisher, wanting to know where he hid his serum. The Punisher replies that he's flushed it down the toilet but, unbeknownst to Magnum, he has the needle of the serum capsule pressed against his forearm, readying himself to inject the serum in his bloodstream. Magnum doesn’t believe the Punisher and asks him if he ever felt compelled to find out what all his hatred and rage, converted into power, would be like; to keep killing and killing until all of it is eaten up. Coming to the realization that it is not something he wants to try, the Punisher crushes the serum capsule between his fingers and proceeds to tell Magnum to kill him already, as he’s sick of hearing his voice. Moses Magnum is about to put a bullet through the Punisher's skull when the hull door bursts open and comes crashing upon him, courtesy of Spider-Man. Before Magnum can get back on his feet, Spidey launches himself at him, engaging him into battle. Nearby, the Punisher breaks free from his bonds and attacks Magnum’s henchmen. He is about to kill him but Spidey prevents him from doing so, telling him to "play nice". Ticked off, Magnum prepares to unleash an earthquake on them but Spider-Man reminds him that they are on a boat, so his powers are useless. Spidey then takes him out with a single blow to the head. The Punisher wants to kill Magnum but Spidey won't let him; Spidey webs Magnum up and hauls him back on the main deck, where all his henchmen have been rounded up and webbed up. Spidey asks the Punisher if he has one of his spider-tracers, since his spider-sense is still tingling; the Punisher reveals that he swallowed one. Spidey asks about the serum. The Punisher reveals that he had it on him in case Spidey didn't come through but it has now been destroyed. Spidey asks the Punisher why he didn’t take the serum, seeing as he had a gun pointed to his head. The Punisher simply replies that it's best he didn't take the serum, because nobody knows what is inside him. Having said that, the Punisher tells Spidey that he’s taking the speedboat. When Spidey starts protesting, the Punisher shoots Moses Magnum in the stomach. The Punisher then tells Spidey to take Magnum to the hospital within an hour, or else he'll die, should he decide to come after him. He then climbs onboard the speedboat and sails away. Spidey grabs hold of Magnum and rushes him to the command centre where he gets stuff from a first aid kit to patch him up until they can get back on land to seek medical help. As Spidey tries to stop the bleeding, Magnum comments that it must be hard for Spidey to save people he doesn't like. Steering the large boat back toward Manhattan, Spidey replies that it sure beats driving a cab!
The end.