After contacting Robbie Robertson to obtain additional information on Congressman Miles and his association with Biotechnix, Peter Parker switched to his Spider-Man costume and met with his super friend, the one and only Daredevil. Using his amazing heighten senses, Daredevil managed to tell Spidey where the "Bio Bug" microchip he picked up at the exhibit came from: the Biotechnix building down in Chinatown. In another part of town, Doctor Octopus was busy working FOR Fusion and building some kind of prosthetic arm of his own. It was revealed that Doc Ock had been working under an assumed name at one of Fusion’s facilities and that Fusion permitted him to remain undetected by the authorities for the simple reason that he needed him for his own evil plans. Doc Ock appeared to be genuinely frightened of Fusion.

After leaving Daredevil, Spidey made his way to the offices of Congressman Miles, where he confronted the latter about his shady connections with the co-owner of Biotechnix and his crooked moves to have bills passed faster at Congress. Spidey left Miles with the looming threat of being exposed to the media. Meanwhile, at some kind of special event, Robbie Robertson tried hard to convince J. Jonah Jameson to investigate Congressman Miles but Jonah appeared hesitant at going ahead with it. Whether Jonah was being paid not to talk about Congressman Miles in the Bugle remains to be seen.

Following the lead provided by Daredevil, Spidey made his way to the Biotechnix building in Chinatown. He entered the building unnoticed and soon came across none other than Doctor Octopus working away at his own version of the prosthetic limb in some kind of laboratory. Spidey dropped down from the ceiling and enticed Doc Ock into a battle. A fight naturally ensued and both arch nemeses fought hard and long, the brawl spreading into the halls and into other rooms. It seemed as though Spider-Man was getting the upper hand but in the last few panels he was knocked out by Fusion who tricked him by using his morphing powers to transform himself into a duplicate copy of Doctor Octopus. The issue ended with Fusion and Doctor Octopus standing over the body of the unconscious Spider-Man.

In Peter Parker Spider-Man #40, Spidey managed to set himself free from the evil doctor's tentacles and made his way out of the building, stealing the prosthetic limb Doc Ock had been working on, along with a suitcase sitting next to the artificial limb. Elsewhere, Robbie Robertson managed to convince J. Jonah Jameson to let him investigate Congressman Miles and his association with Biotechnix.

Spidey opened the stolen suitcase and found some incriminating evidence and other relevant information. He met with Nick Fury of S.H.I.E.L.D. and the two exchanged information about what Spidey found in the suitcase (i.e. a note with the words "John Hancock" and "GL-52" written on it). It is revealed through their conversation that the "John Hancock device" was stolen by a recent amputee who was reassigned to the Groom Lake military facility referred to as GL-52. It is also revealed that this device can allow its user to track down certain types of individuals based on their personal radiation signature. Also revealed during their conversation is that the T-137 prototype prosthetic arm can act as two-way receiver to the brain of its recipient and that consequently, any lunatic who would decide to keep tabs on his evil empire using mind control would have an army of amputees walking around the country doing his bidding.

Elsewhere, the individual who stole the "John Hancock device" delivers it to none other than Fusion and Doctor Octopus. Fusion beams with pride that he's got the device and as a result will be able to track down Spider-Man. Doctor Octopus however, has other plans. First, he grabs the "thief" and drives one of his tentacles right through his chest, killing him instantly. Then, as an angry Fusion turns around to confront his servant – or so he thought – Doc Ock grabs the latter and begins pummelling him to a bloody pulp, going as far as crushing his head using his mighty tentacles.

Meanwhile, a television newscast breaks out the news that all hell is breaking loose for Congressman Bradley Miles who was arrested for alleged fraud and stock manipulation from within his Manhattan office. As well, the newscast reveals that executives of Biotechnix were also being investigated for having links to members of organized crime and that Biotechnix’s founder and C.E.O., Amos Peter, may have been involved in recent breaches of security at an undisclosed military installation. Spider-Man hears the news but knows that with Fusion and Doctor Octopus at large, it cannot be over. He decides to check out other Biotechnix storage facilities. He arrives to the facility near the Hudson River and enters the building unnoticed. He makes his way down a dark corridor where he makes the gruesome discovery of the "thief", who lies dead in a pool of his own blood. Spidey follows the trail of blood back to its origin and finds Fusion strung up to the ceiling with four prosthetic limbs pinned into his sides, blood gushing out of his body. This is where this issue picks up.

ACT 1: Spidey unties Fusion and checks his pulse; fortunately he is still alive, however barely. Spidey uses his cell phone and calls 911. The he tries to find some clue that could help him track down Doc Ock. He notices some kind of material stuck to the bottom of Fusion's foot and realizes that it is some kind of pliable building wrap used for insulation. He uses his cell phone once again and calls Matt Murdock, a.k.a. Daredevil to help him find out where the material may have originated from. At first reluctant to help because he once represented a former employee in a lawsuit brought against Biotechnix, Matt finally provides Spider-Man with an address.

ACT 2: Meanwhile in downtown Manhattan at the site of a Biotechnix building under construction, Doctor Octopus is on the phone with two gentlemen (holding a large suitcase) that wish to buy the "John Hancock device". Doc Ock instructs them to take the access elevator located at the center of the building and to meet him at the highest completed floor. The gentlemen climb in the elevator and begin their ascent. As they make their way up, they discuss killing Doc Ock once the deal is done. The elevator finally reaches the highest completed floor where Doc Ock is waiting. The elevator door opens and the evil doctor's jaw drops to the floor. Both men are unconscious and wrapped up in webbing. A voice is heard and Doc Ock turns around, and comes face to face with Spider-Man who is holding up the suitcase that the two men were carrying. Spidey tells Doc Ock he's just realized that him and Fusion weren't going to use the "John Hancock device" to track him down but rather to sell it to the highest bidder. Furious, Doc Ock replies that there is 30 million dollars worth of diamonds in the suitcase that belong to him and that he wants Spider-Man to hand it down. Of course, Spidey refuses to hand over the suitcase and naturally a battle ensues. The fight rages on for several pages, both opponent giving it their best shot. At one point, Spidey gets knocked out by Doc Ock and falls several floors down. Thinking that he's defeated the wall-crawler, the evil doctor simply walks back to the "John Hancock device" and stares proudly at it with a large grin on his face. Suddenly however, Spidey shows up and takes the device away from Doc Ock. He then climbs all the way up to the highest point of the building and waits for his rival to arrive. Seconds later, Doc Ock shows up and tries to take the device away from Spider-Man. Having had enough, Spidey smashes the device into the elevator motor, which begins shooting bursts of electricity. Infuriated, Doc Ock attacks Spidey and tries to strangle him. Spidey fights back and electrocutes the evil doctor, who starts to fall towards the ground below, hitting beams and columns along the way, which break his tentacles into pieces. Fortunately for the latter, his sole remaining tentacle saves him from imminent death when it clutches onto a horizontal beam. Spidey drops down on a webline and comes to Doc Ock's side. Doc Ock pleads to Spider-Man to help him but the wall-crawler replies that for once, he will make an exception and not help him. At that exact moment, Doc Ock's remaining tentacle gives up and he starts to fall down towards the ground. Suddenly however, a web-line appears and saves the evil Doctor. Spidey just couldn't let him die.

ACT 3: Later that day, Spidey meets with Nick Fury and gives him what's left of the "John Hancock device". He then tells him that Doc Ock along with 30 million dollars worth of diamonds are waiting for him at the Biotechnix building under construction in downtown Manhattan. Nick Fury thanks him and the wall-crawler web-slings away.