Peter Parker/Spider-Man finds Ben, just as the Jackal impersonator returns. The impersonator leads them through the previously guarded passage and into the laboratory. The Guardian is in the lab and appears to be in great pain. Blaming the real Jackal for his condition, he collapses. The impersonator proceeds to take off his mask and that of the Guardian, revealing that they are both failed clones of Peter Parker. Suddenly, a voice calls out to the impersonator, telling him not to compare himself to either Ben or Peter, because "they" are his greatest achievements. With that said, 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 a clone.

The Jackal 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.

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. 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?

Making his way across the city, Kaine is tormented with the recent revelation that there is a third Peter Parker. Suddenly, 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.

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. Robbie is all out but promises to scrounge something up for him. While there, Peter 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.

After leaving the Bugle, Peter is confronted by Kaine, who hands him a copy of the disk he 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 he 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 prepares to leave the gym where he is watching Flash Thompson coaching, the Jackal and Jack show up, looking for a fight. Ben ducks out, transforms 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.

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.

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.

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 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 adage that "with great power must come great responsibility”".

While walking along a street, Mary Jane is confronted by Judas Traveller. 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 contemplates the most recent developments and ponders that he could not have planned it better...or did he?

At the Parker apartment, Mary Jane Parker and Ben Reilly have a heart-to-heart conversation. Ben comments to MJ that she should get the baby tested as soon as possible (it was revealed that the baby may have genetic damage) and suggests a doctor-friend of his who specializes in genetics: his name - Seward Trainer. Ben earns her trust.

While the above events take place, Peter Parker, who is imprisoned, contemplates breaking out of prison. He quickly realizes that, in doing so, he would jeopardize the lives of Mary Jane and their unborn child; thus he decides to stay put for now.

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 topple over due to the surge of water. Escaping back to the surface, Mary Jane comes face-to-face with...Peter Parker.

Meanwhile, at the Parker home, MJ 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 MJ 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.

Meanwhile, MJ 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, MJ tries to get away. Ben continues the assault on Kaine, while Peter goes after MJ, 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 MJ are about to turn around and escape when Kaine comes in between them and the only exit.

Peter Parker, wearing Ben's Scarlet Spider costume, is attacked by the Beetle, while heading back home. As they battle, Peter loses his web-pack, which contains the black costume. The pack is found by the police and Daily Bugle reporter Ken Ellis, who recognizes the costume and wonders how the Scarlet Spider got hold of it.

In prison, Ben tries to adapt to his new life when he gets an unexpected visit from Felicia Hardy, the Black Cat, who Ben does not recognized, having never met her before. Felicia quickly realizes that something weird is going on and wonders what happened to Peter.

Elsewhere, Detective Jacob Raven and Stunner, are taking aim at members of the underworld to try and find out more about the mysterious Kaine. Though Stunne's methods of interrogation are a little more violent than his, Raven does not mind because he wants Peter to be exonerated by any means.

In another part of the city, Kaine attacks the Hobgoblin, unprovoked. The Hobgoblin is soon rescued when his fellow super-villains arrive on the scene, though none of them are able to take Kaine down. In comes Peter, as the Scarlet Spider, who jumps in the mêlée. The battle eventually ends and everyone escapes relatively unscathed. Peter makes the decision to help Ben no matter what, which is why he must find Kaine before he can become a threat to him and MJ.

Speaking of MJ, she receives a call from Dr. Seward Trainer, asking that she come over to his lab to go over the genetic tests they took earlier. She meets with him and whatever it is that he tells her, she quickly runs away, seemingly worried about something.

Later that same night, the mysterious Scrier appears at the scene of the fight that occurred between Peter, Ben, Kaine and the third Peter Parker. There, he finds a pile of goo with shreds of a Spider-Man costume in it. Scrier grabs it, believing that it may be of some use down the road.

A car carrying Professor Warren and the Gwen Stacy clone is crossing the George Washington Bridge, the infamous bridge where the original Gwen Stacy met her demise at the hands of the Green Goblin. The car suddenly crashes, almost tumbling into the water down below. The new Green Goblin (later revealed to be Phil Urich, nephew of Daily Bugle reporter Ben Urich) swoops in and rescues Gwen, though it looks like he is kidnapping her. He transports her to the top of one of the bridge's pedestals where he drops her off. Warren starts shooting at the Goblin and causes Gwen to lose her balance and fall off the pedestal. Thankfully, the Scarlet Spider arrives on the scene and rescues her. After getting her to safety, he goes to check on Professor Warren, only to find that he's degenerated and the Green Goblin has gotten away. In the ensuing confusion, Gwen leaves.

In this other reality, Traveller claims to have captured Aunt May’s soul and tests Peter's heroism by questioning whether he would be willing to sacrifice the lives of several others to return his aunt to life. Peter refuses to go along with Traveller's insane proposal, telling him that he is not a God, nor can he be believed. Traveller admits that he is not a God, but he is very close to being one. He proceeds to take Peter 24 hours forward in time to witness the reality then. To his utter shock (Peter’s), New York City is completely destroyed. The reason for the destruction: Peter.

The vortex is starting to close in on Traveller, which it originated from. Scrier reveals that Peter and his family will remain safe, as they are protected by the last of Traveller's powers. However, the city will be destroyed and Traveller will die. As the vortex tries to engulf Traveller, the Scarlet Spider (i.e. Peter) reaches in and grabs him out of the vortex, saving his life. As Scrier claims the unconscious body of his ally, he tells Peter that Traveller will never be satisfied until he can completely understand him. Peter accepts that and goes back to his wife and holds her close as Scrier and Traveller disappear.

Spidey and the Green Goblin reluctantly join forces to save the homeless man that Firefist is about to kill. While the Green Goblin swoops down and saves the bum, Spidey engages into battle with Firefist. After dropping the homeless man off to safety, the Green Goblin returns to aid the wall-crawler, unaware that the Jackal is watching him from a distance and has deduced that whoever is behind the mask is not an Osborn. After fighting valiantly, Spidey and the Green Goblin manage to defeat Firefist. Before Spidey can catch him, the Green Goblin takes off into the night, vowing to fight the good fight and become a superhero. After delivering Firefist to the authorities, Spidey swings off into the night and heads back home, where he intends to have a long awaited heart-to-heart talk with MJ about their baby. Unbeknownst to him, the Jackal continues watching and, after a while, returns to his laboratory where he is greeted by another Peter Parker.

Detective Raven and Stunner arrive on the scene of the Spider-Man/Kaine battle. Stunner prepares to jump in the mêlée but before she or Raven can do anything, Judas Traveller appears and teleports both Kaine and Spidey away from the area.

Spidey understands where Kaine is coming from but still cannot believe that he would not help Ben Reilly. Running out of options, Spidey realizes that the only way to save both Ben and clear his name is to reveal his identity to the world and explain everything about the whole clone saga (a feat, not the least). Kaine begs him not to do it but Spidey ignores him and enters the court to offer new evidence that will prove Peter Parker's innocence. He starts to pull his mask off when Kaine interrupts him and approaches the judge's bench to come clean. Kaine tells the judge and the whole court that he has hated Peter Parker ever since Parker took a picture of him while committing a murder and that, to get his revenge on him, he altered his fingerprints to match his, so as to implicate him in his most recent murders. Having said that, Kaine lets the court take his fingerprints as evidence to support his claims. Kaine will not go down that easy however and he sets out to do what he has wanted to do for years, which is to carry out Ben Reilly's execution. At issue's end, he lunges himself at Ben, who is in fact impersonating Peter Parker, which is a fact that Kaine does not seem to know...yet.

Elsewhere, the Jackal is ready to begin mass-producing his new and improved Carrion virus. But he needs one last ingredient before starting, so he gives the third Peter Parker a costume he made for him and sends him on his way to retrieve said ingredient.