Back in New York, Peter Parker is in the process of altering his life insurance policy to include the baby, unaware that Detective Raven (seen mostly in the other Spider-Man titles investigating the death of his partner at the hands of Kaine) is meeting with J. Jonah Jameson. He does not notice them because he is too busy dealing with strong memory flashes of him waking up inside a cryogenic chamber. Wanting to make sense of all this, he dons his costume and goes out for a swing. While web-slinging across the City, he tries to understand why he is having those memories, and comes to the realization that the only plausible explanation that seems to make sense is that he is the clone. Yet, he cannot bring himself to accept that. Suddenly, he gets a vision of the Scarlet Spider lying unconscious and realizes that he must try to save him.

In Amazing Spider-Man #399, Kaine prepares to make his move when he is confronted by Scrier last seen in Spectacular Spider-Man #217. Kaine is evidently taken aback by his arrival, as it appears that Scrier is in the know regarding Kaine's relationship with Ben Reilly/Scarlet Spider. Scrier tells Kaine that he should not fear him...yet.

Peter Parker/Spider-Man reaches Ben, as the latter slowly regains consciousness. As they exchange pleasantries, the Jackal impersonator returns and leads the two of them through the previously guarded passage and into a laboratory. The Guardian is in the lab, though it appears that he is in great pain. As he blames the real Jackal for this, he collapses. The Jackal impersonator takes off his mask and that of the Guardian revealing that they are failed clones of Peter Parker. Just then, a voice calls out to the impersonator, telling him that he should not compare himself to either Spider-Man or the Scarlet Spider because they are his greatest triumphs. Having said that, the real Jackal steps out of a regeneration chamber, more powerful than ever, and reveals that the Jackal that died years ago, in the now classic Amazing Spider-Man #149 was also a clone.

The Jackal proceeds to tease them and tells them that degeneration affects all clones sooner or later. Spider-Man asks the Jackal if that means Ben will die soon and the Jackal replies that he was referring to the both of them. Hearing that, Spider-Man loses it. Ben tries to calm him down but Spider-Man turns his anger towards him. Seeking the truth, Spider-Man asks the Jackal to prove it. The Jackal agrees and proceeds to open another cryogenic chamber. As it opens, the Jackal reveals to them that he's made a mistake and accidentally opened the wrong one. The one he opened contains the real Gwen Stacy.

In Spider-Man Volume 1 #56, Spider-Man goes off to talk with Gwen Stacy, while Ben Reilly/Scarlet Spider confronts the Jackal, who tells him that he is the real Peter Parker and that he should kill his clone and reclaim his life. While this takes place, Kaine watches from above and Scrier watches above him.

The Jackal and his impersonator attack Ben so Spider-Man comes to his aid. While they battle, the Jackal tells Spidey that he is the real Peter Parker and that Ben is the clone and tells them both that he was lying to Ben moments earlier just for kicks. Spidey accuses him of lying because he read his journal and spoke with the High Evolutionary. The Jackal comments that the High Evolutionary would have absolutely no purpose in telling him the truth and goes on telling him to go to Gwen, as she is his true love. Gwen approaches him (i.e. Spidey) and wraps her arms around him and she tries to convince him that she is real. But, as she does so, she degenerates right in front of him, to the utter laughter of the maniacal Jackal. Spider-Man and the Scarlet Spider prepare to move in on the Jackal but he manages to flee through an escape door, telling them that the entire building is set to explode and that neither of them is the real Peter Parker; the real Peter Parker is in a chamber somewhere in the building. Spidey and the Scarlet Spider safely make their way out of the building before it explodes but Spidey is angry still, because he wants to know the truth. Ben tells Spidey that it is probably easier just to go on living. At issue's end, it is revealed that a lone cryogenic pod rests. But what or who is inside it?

In Spectacular Spider-Man #222, Kaine rummages through the wreckage of the Jackal's lab and finds a computer from which he copies pertinent files onto a floppy desk. But as he does so, he accidentally triggers the emergence of a genetic pod containing a third Peter Parker. On cue, the Jackal and his little apprentice, Jack, appear and confront Kaine. While Kaine battles the Jackal, Jack makes a duplicate disk of the information Kaine downloaded from the computer. Just then, Scrier, last seen in Spectacular Spider-Man #217, chooses that moment to show up and interrupt the whole shindig. Kaine uses that opportunity to flee the scene and so does the third Peter Parker. While all this takes place, Ben Reilly, a.k.a. the Scarlet Spider, is watching Flash Thompson coach basketball to a bunch of kids and somehow envies his life.

As Kaine makes his way across the city, tormented with the recent revelation that there is a third Peter Parker, he gets a vision of Mary Jane lying dead on the ground. Several blocks from there, a very much alive Mary Jane is visiting her family doctor who informs her that he's detected a minor anomaly with the baby-to-be and he'd like to schedule some additional tests as soon as possible.

While the Jackal oversees the setting up of his new laboratory, Peter Parker meets with Robbie Robertson at the Daily Bugle to try and score a photo assignment. Unfortunately, Robbie is all out but promises to scrounge something up for him. While there, Peter also runs into J. Jonah Jameson who informs him that a police detective has been around asking questions about him and Ben Reilly. As these events take place, several miles away to the West (presumably in Utah), a warrant is in the process of being issued for the arrest of whomever killed Detective Raven's partner.

As Peter Parker walks along a street, he is confronted by Kaine who hands him a computer files he recently stole from the Jackal's lab and tells him that the files contain proof that he is the real Peter Parker. Kaine disappears as quickly as he showed up but is there long enough to ruffle Peter's feathers, who is tired of all these mysterious strangers showing up and screwing with him. Peter takes off after Kaine.

As Ben Reilly prepares to leave the gym where he was watching Flash Thompson in action, the Jackal and Jack show up, looking for a fight. Ben ducks out, changes into the Scarlet Spider, and comes back to confront the Jackal. Several blocks from there, Peter, as Spider-Man, catches up to Kaine and confronts him, demanding to know the truth. Meanwhile, the third Peter Parker, recently released from a genetic pod is heading somewhere, still dazed from being in the pod and trying to remember who he is and what he should be doing.

In Web of Spider-Man #123, the issue features two major battles: Spider-Man versus Kaine and the Scarlet Spider versus the Jackal. Though the Scarlet Spider struggles difficultly into defeating the Jackal, he finally succeeds into overpowering him and taking him into custody. The Jackal is sent to Ravencroft, which is exactly where he had planned to be sent, as there is something there that belongs to him. Jack, the Jackal's apprentice, gives the Scarlet Spider the floppy disk containing information about the real Peter Parker. Upon seeing this, the Jackal snaps his fingers, causing Jack to degenerate right in front of the Scarlet Spider. Seconds before crumbling into dust, Jack tells the Scarlet Spider that his future is now in his hands.

While this takes place, Spider-Man has his hands full with Kaine, who is extraordinarily powerful. The battle goes on for quite a while, until Kaine gets the upper hand and knocks him out. Kaine then disappears into the night.

Meanwhile, at the Forest Hills Hospital, Aunt May awakens from her coma, though she does not answer to any of the doctors. Her thoughts reveal that she wants to see Peter as soon as possible. Meanwhile, in Utah, Detectives Trevayne and Raven are eagerly awaiting the aforementioned warrant to be issued, but it hasn’t come through yet.

At issue's end, Ben finds himself atop the smokestack, where the first confrontation between Spider-Man and him ended. He wonders whether the floppy disk obtained from Jack will reveal any secrets or simply offer more questions. Truly believing himself not to be the real Peter Parker regardless of what is on the disk, Ben throws the disk into the river and swings off into the night, knowing that truly "life is in the living". Elsewhere, the third Peter Parker returns to New York City, still dazed and confused, and wanting to rest before confronting his inevitable destiny.

In Amazing Spider-Man #400, Aunt May, having emerged from her coma in Web of Spider-Man #123, returns home to Peter and Mary Jane. Upon seeing Mary Jane, Aunt May intuitively and immediately deduces that she is pregnant and gives them words of advice, à la Uncle Ben.

Ben Reilly visits Peter and they have a heart-to-heart conversation in Aunt May's yard. Ben tells Peter that he is leaving New York because he does not want to ruin his or MJ's life since things seem to be going so well. As Ben leaves the house, his thoughts reveal that he may have been in love with a woman named Janine.

A week later, Peter takes Aunt May atop the Empire State Building, as per her request to get out of the house. Looking out the observation deck, Aunt May asks Peter how it feels to swing over the City and being so free. Peter is taken aback and tries to change the subject but Aunt May tells him that she would have had to be an idiot to not know that he is Spider-Man, especially since they lived under the same roof for so many years. She explains to him that, after Uncle Ben passed away, she could not accept that he was risking his life every day as Spider-Man. But it grew on her and she is now very proud of him and knows Ben would be as well, if he were still alive. Shortly after revealing this, Aunt May collapses, so Peter takes her home. A short time later, after having said her goodbyes to Peter, Mary Jane and Aunt Anna, Aunt May passes away.

Family and friends come to pay their respect to Aunt May in what is one of the most emotionally charged issues of Amazing Spider-Man ever written. A short time after the funeral, at the Parker house, Detectives Trevayne and Raven show up and arrest Peter for first-degree murder.

Trying to figure out what to do to help Peter, Mary Jane thinks about calling Matt Murdock, a.k.a. Daredevil, but believes him to be dead. As she prepares to go to the police station, the Scarlet Spider shows up at the house, removes his mask, introduces himself as Ben Reilly, and tells her that the time has come for them to meet face-to-face.

In Spider-Man Volume 1 #57, Mary Jane is not at all pleased to see Ben Reilly and accuses him of causing more damage than helping. Though Ben leaves her, he promises to help nonetheless.

Peter is held without bail and is paid a visit from Detective Raven, who informs him that he won’t get away from killing his former partner.

Meanwhile at the Daily Bugle, Robbie Robertson asks J. Jonah Jameson what he is planning to do regarding the Parker story and if he intends to help the Parkers at all. Jonah does not really answer Robbie but it is later revealed that Jonah is privately paying all of Peter's legal fees.

While the third Peter Parker wanders the streets in search of answers, the jailed Peter Parker seeks answers from his wife, Mary Jane. He does not understand why he has been arrested for a crime he knows he did not commit. Elsewhere, Detective Raven is starting to come to the realization that he might have arrested the wrong man. While all this takes place, Kaine is continuing to have visions of Mary Jane dying.

The third Peter Parker comes under attack by a street thug but is able to get away when he discovers that he has powers and also remembers Uncle Ben's old and infamous adage that "with great power must come great responsibility".

While walking along a street, Mary Jane is confronted by Judas Traveller, last seen in Spectacular Spider-Man #217. Traveller wants to understand Spider-Man through the eyes of the woman who loves him. Thankfully for her, the Scarlet Spider had been following her so he drops to protect her. Though Traveller is excited to meet Ben again, the timing could not be any worse. Snapping his fingers, Traveller causes the street to explode and buildings to collapse, which preoccupies the Scarlet Spider. Traveller prepares to leave with Mary Jane in tow but Ben grabs Traveller's wrist before he can escape. Realizing that Ben will not give up that easily, Traveller releases Mary Jane and tells Ben that "Soon, very soon...you, Peter, and I will sit down together and get to know all about one another". He then disappears. Ben apologizes to MJ for intruding and she tells him that she is willing to try and talk to him.

At issue's end, Kaine visits Detective Raven and tells him that he has arrested the wrong man. Raven replies that all evidence points to Peter Parker so Kaine puts his hands on Raven's face and gives him a non-lethal mark similar to that found on his other victims. He then proceeds to tell Raven to take a good look in the mirror and think about the evidence some more.

Meanwhile at Ravencroft, the Jackal, send there in Web of Spider-Man #123, contemplates the most recent developments and ponders that he could not have planned it better…or did he?

At the Parker apartment, Mary Jane sits down at the kitchen table with Ben Reilly so they can have a talk about what is going on. Ben takes his Scarlet Spider mask off to drink his tea but Mary Jane asks if he can keep it on, because she cannot bear looking at another man wearing Peter's face. Ben agrees to keep the mask on to prove that he can be trusted.

Meanwhile, in prison, Robbie Robertson visits Peter and tries to convince him to tell his side of the story by using the Daily Bugle. Peter, however, cannot accept, as he would have to reveal his secret identity and nobody would believe that a genetic duplicate of himself committed the crime he is being indicted for.

At the hospital, Detective Trevayne reassures a bandaged Detective Raven that they will find whoever attacked him (it was Kaine but Trevayne doesn't know that yet). Raven replies that he "blew it" so Trevayne asks why he is saying that. Raven replies that they put the wrong man behind bars. Trevayne is in disbelief and tells Raven that they nailed the right guy and that, on fingerprints alone, a jury will convict him. Raven unwraps the bandages covering his head, revealing the mark of Kaine plastered on his face.

Elsewhere, the third Peter Parker picks up a newspaper while walking along a street. The headline reads "Bugle Photographer Arrested" with a photo of Peter Parker underneath. The name sounds familiar to him and he wonders where he's heard it before. Instinctively, he realizes that he has some unknown mission to accomplish, a task of great responsibility. As he walks away, he has no idea that a silent stalker is watching is every move.

Back at the Parker apartment, Ben tells Mary Jane that she has to act responsibly and get the baby tested as soon as possible. Ben suggests a doctor-friend of his, who specializes in genetics; his name: Seward Trainer. MJ wonders how he knows something could be wrong with the baby and comes out asking why he is trying to help them and why he even cares if something happens to them or the baby.

Back in prison, Peter wonders if Ben is responsible for the Salt Lake City murder, which he's been arrested for. He contemplates breaking out of prison and going after his clone, however, for fear that it would give away his secret identity and destroy any chance of a normal life for Mary Jane and their future child, he decides to stay put for now.

At Ravencroft, guards are keeping an eye on the inmates via a closed circuit camera system. While the Jackal sleeps soundly in his cell, Carnage is going crazy in his. The reason being that the Jackal is actually walking by his cell and not sleeping after all. As he enters Dr. Kafka's office, it is revealed that the Jackal penetrated the Institute's computer system and programmed it with a video loop of himself sleeping in his cell. He sits at her desk and accesses Dr. Kafka confidential files with the intention of learning why a former associate of his recently evidenced an interest in Ravencroft. He pulls out the file of Malcolm McBride, a.k.a. the second Carrion (McBride was a former student of Professor Miles Warren who became Carrion but who lost his power when Shriek absorbed them in Amazing Spider-Man #393). It seems that he's found exactly what he needs.

The third Peter Parker is walking along a street and ends up at an abandoned warehouse, the same infamous warehouse where Spider-Man captured the burglar that killed Uncle Ben. He somehow recognizes the building as the site of a critical juncture, a fateful turning point that helped define his entire life. Clutching his newspaper, he suddenly realizes where he must go to find the answers he so hungrily seeks. He takes off into the night, unaware that he is being watched by Scrier.

Back at the Parker apartment, Ben tells Mary Jane that he and Peter are in competition for the same life, however, he has come to terms with who and what he is and does not want to compete for the same life anymore. He goes on explaining that, as a clone, he does not get to live as long as real people, because he came with a degeneration factor and it is only a matter of time before it catches up to him. He tells her that's why he is so eager to help them. With that, he's earned Mary Jane's trust and she removes his mask.

Back at Ravencroft, the security guards notices that the camera in Shriek's cell seems to be dead. He goes out to investigate. Unbeknownst to either guard, the Jackal has killed the camera and is attacking Shriek. Since he developed the Carrion virus all these years ago, the Jackal has come to claim what's his. Though she defends herself admirably, the Jackal overpowers her and knocks her out. Though it is not shown, the Jackal appears to extract the Carrion virus out of her. The guard finally reaches the cell but the Jackal had been waiting for him and with a single blow to the head, the guard is killed. The Jackal makes his way out of the building with no one any wiser.

Meanwhile at the prison, Peter continues to wonder if Ben is a murderer, however, he comes to the realization that if Ben is really his clone, and if there is even the slightest vestige of Peter Parker within him, then Ben cannot be a murderer.

The third Parker makes his way to the cemetery where he finds the graves of Aunt May and Uncle Ben. Falling to his knees, he is bombarded with searing images of his past. Images of his Aunt May and his Uncle Ben and himself, as Spider-Man, web-slinging thirty stories above the ground. As image builds upon image, and memory feeds memory, he remembers who he is. He is Peter Parker. As he comes to realize that, he grabs the newspaper featuring the story about the Parker arrest and figures that the Peter Parker they have in jail must be some kind impostor. The article mentions that he is married to Mary Jane so it appears that he goes out to find her and the two of them go out for a walk (though I am not sure if the Peter Parker walking with Mary Jane is in fact Ben Reilly or the third Parker). Unbeknownst to either of them, the mysterious Kaine watches on.