Meanwhile, in prison, a fire breaks out and Peter uses his abilities to save the other prisoners. Elsewhere, Detective Jacob Raven is confronted by Stunner who offers to help him find the real killer of his partner and her lover, Doctor Octopus.

Minutes after leaving Trainer's lab, Mary Jane is abducted by Kaine and taken into the sewers. Kaine warns her that he life is nearing the end but before he can say more, she turns a nearby drain on, forcing Kaine to fall over due to the surge of water. Escaping back to the surface, Mary Jane comes face-to-face with...Peter Parker.

In Amazing Spider-Man #401, Part Two of the Mark of Kaine storyline, the story opens up with Mary Jane coming face-to-face with the third Peter Parker. She does not know whether this Peter Parker is her husband or Ben Reilly. The third Parker explains that he is neither and tells her that he has been locked away for the past five years while an impostor has stolen his life. The mysterious Kaine, who was last seen in the sewers, shows up on the scene and warns Mary Jane about the third Parker. A battle ensues between Kaine and the third Parker, creating an opportunity for Mary Jane to get away.

Moments later, Mary Jane calls Ben and gives him a rundown of the latest developments. While this takes place, the jailed Peter Parker is visited by one of Judas Traveller's associates, who lets him know that Mary Jane is in danger. Wanting to protect his wife no matter what, Peter decides to breakout, regardless of the fact that it could damage his reputation and make him look guilty should he get caught. He manages to make his way out of his cell undetected and, as he stands outside the prison walls, Traveller shows up and offers to help by putting an illusion of Peter Parker in his cell, while he goes out to save Mary Jane. With Peter Parker gone, Scrier appears and questions Traveller's fascination with Peter Parker.

Meanwhile, at the Parker home, Mary Jane has bought herself a gun for protection, mainly because it appears that there are even more characters that know Peter's secret identity; therefore putting her life in jeopardy. She is taken aback when she runs into Spider-Man in the house, especially when he reveals himself to be the third Parker. Mary Jane warns him to stay away as he draws near. She fires the gun and misses him, and the force of the blast causes her to lose control. On cue, Kaine appears to take out the third Parker. He contemplates killing him but a noise coming from upstairs stops him in his tracks. He grabs hold of Mary Jane and quickly leaves, heading towards his secret underground hideout. The noise Kaine had heard turns out to be the Scarlet Spider entering the Parker home through the rooftop skylight. Scarlet Spider wonders what Peter is doing home – it's actually the third Parker but he doesn't know that yet – just as the jailed Peter who escaped from prison enters the home and all three come face-to-face.

In Spider-Man Volume 1 #58, Part Three of the Mark of Kaine storyline, the story opens up with the tree Peter Parker facing each other and trying to make sense of all the confusion. Ben Reilly/Scarlet Spider comments that he is certain that he – himself – is not the real Peter Parker. He turns to the third Parker and asks what happened. Injured from his battle with Kaine, the third Parker passes out. Ben turns to (the escaped) Peter and asks what he is doing out of prison. Peter reveals that he is going to look for his wife and, on that note, he grabs the gloves and mask of his old black costume and a pair of spare web-shooters and he takes off. Ben goes to take care of the third Parker but the latter has disappeared, in his Spider-Man costume.

A short time later, Peter, wearing the old black costume, comes to rest on a rooftop, waiting for some kind of sign from Mary Jane. He is accompanied by Ben, who offers to help, knowing full well that Peter will need all the help he can get to take on the mysterious Kaine. Meanwhile at Kaine's secret hideout, Mary Jane tries to get answers from Kaine but to no avail. She reaches insider her pocket and pulls out a spider-tracer designed to emit high frequency waves to be used in the event of an emergency. She activates it and seconds later, Peter receives the signal and begins tracking its source to find her. As he takes off from the rooftop, he warns Ben to stay out of it. Elsewhere, the third Peter Parker, wearing a Spider-Man costume, is resolute not to let the other two get the better of him (he believes himself to be the real Peter Parker and the other two to be fakes).

Peter and Ben follow the spider-tracer signal, which leads them into the sewers. Ben tells Peter that he will go in first to distract Kaine while he – Peter – takes care of rescuing Mary Jane. As they prepare to make their move, the third Peter Parker appears and tells them that he will find Mary Jane and kill whoever took her. He suggests that they leave him and Mary Jane alone (again because he believes himself to be the real Peter Parker).

Meanwhile, Mary Jane is on the run from Kaine, who seems to want to carry out with killing her so as to fulfill his visions of her death. Just then, Peter, Ben and the third Peter Parker show up and simultaneously lunge at Kaine. Confused as to who the real Peter Parker is, Mary Jane tries to get away. Ben continues the assault on Kaine, while Peter goes after Mary Jane, with the third Peter Parker in tow. The third Peter Parker starts to lose it and he screams at them that he is the real Peter Parker and that he will kill everybody else. Peter and Mary Jane are about to turn around and escape when Kaine comes in between them and the only exit.

Outside the prison where Peter was incarcerated, Judas Traveller gets a visit from Scrier who asks how much longer he is going to wait out there. Traveller replies that he will wait as long as it takes because he chose to aid Peter because the lives of his wife and unborn child are at stake. He also explains that he does not wish to see Peter destroy whatever chances he may have had for a decent life by escaping prison. Scrier comments that, as powerful as he – Traveller – is, he will not be able to maintain the illusion of Peter Parker sleeping within his cell for an indefinite period of time. Scrier asks what he will do if Parker does not return. Traveller replies that Peter's sense of responsibility is too great and that, as a result, he will make the right choice and come back.

The battle rages on between Kaine and the Scarlet Spider and the third Peter Parker who now has the ability to morph his body at will. Kaine manages to drop down the ceiling on the third Peter Parker but that only slows him down momentarily. Using his ability to recode his DNA, the third Peter Parker extracts himself from the rubble and continues his attack.

Peter and Mary Jane escape back to the surface, where Mary Jane gives Peter her blessing to go back into the sewers to help Ben.

Kaine and the Scarlet Spider try to take down the third Peter Parker but to no avail. Realizing what he and Kaine must do, the Scarlet Spider recommends that they lead the third Peter Parker outside, where they will have more room to maneuver. Kaine reluctantly agrees.

On the surface, Peter promises Mary Jane that he will go back to prison once he helps out Ben and that the two of them will reunite soon.

Kaine and the Scarlet Spider finally make it to the street. Within seconds, the third Peter Parker comes crashing through the thick layer of asphalt and dirt separating the sewers and the road surface. Just then however, a steel girder soars through the air and impacts the third Parker in the chest. Several stories up, Peter, wearing the mask of his old black costume, has built a catapult made of web and he is slinging beams at the third Peter Parker. The third Parker grabs hold of a nearby car and throws it at Peter. Quickly, Peter dodges the incoming car. But then, the third Parker lunges at a nearby propane truck and prepares to throw it at them. Prepared to do what neither Peter or Ben would do, Kaine grabs hold of a nearby car and hurls it towards the third Parker. The impact is disastrous, as the propane truck erupts in a giant ball of fire, seemingly killing the third Peter Parker. As Peter wonders what happened to Kaine and Ben. Kaine appears through the flames and stares at him, as if he is deliberately trying to taunt him. He then disappears back into the flames. Just then, Peter spots Ben's hand emerging through a nearby pile of rubble. Peter heads over and helps him out of the wreckage. Ben suggests that they go in pursuit of Kaine but Peter verbally lashes out at him because he has to go back to prison, where he is awaiting trial for a murder he believes was committed by Ben. Ben replies that he is innocent and to prove it, he offers to trade places with Peter; he trusts that Peter will do everything in his power to establish his innocence and is willing to bet his life on it. While this takes place, Kaine watches on.

A short time later, Ben goes to prison to take Peter’s place, while Peter returns home to Mary Jane. As Ben sneaks back inside the prison, Scrier and Judas Traveller watch on and it appears that they had anticipated the substitution.

To be continued in Spider-Man Unlimited #9.