Meanwhile in Springville, Pennsylvania, a man has apparently survived the mass Carrion viral infection that wiped out the whole city. The Jackal wants to know why the virus did not kill that man so he sends Spidercide to get him. Spidercide finds the man but runs into the New Warriors, a group of superheroes; a battle naturally ensues. Just then, the Scarlet Spider arrives on the scene. The New Warriors think the Scarlet Spider is an ally of Spidercide so they attack him. As Spidercide is not supposed to get involved with any of them, he takes his leave, sans the survivor. The Scarlet Spider and the New Warriors set aside their differences and try and stop Spidercide and rescue the survivor. Unfortunately, they fail on both counts; Spidercide changes his genetic structure and manages to easily escape and capture the survivor as well.

Back in New York City, Peter Parker is packing his bags and preparing to leave. He has come to the realization that Mary Jane and the baby are better off without him so he picks up his Spider-Man costume and tells himself that he may not be the clone or the original Peter Parker, but he is still Spider-Man. He heads over to the Empire State Building, to recollect about his last moments with Aunt May. As he stands on the top deck of the building, he is interrupted by the Jackal, who taunts him into a fight. As they battle, the Jackal tells him that he is going to bring the world to genetic perfection through cloning and mentions that he could use his help (meaning Peter's). The Jackal extends his hand, telling Peter that it would give his life new purpose. Peter remains speechless and takes the Jackal's hand.

In Web of Spider-Man #127, Part Two of Six of the Maximum Clonage storyline, the Jackal and Spider-Man discuss their newfound alliance when a SWAT team and the Punisher arrive on the scene. Spidey grabs the Jackal and takes him to safety, leaving a confused Punisher behind.

While all this takes place, Mary Jane worries about the effects that Peter being the clone may have on their unborn child.

Spider-Man and the Jackal take to the streets so that Peter can digest the information that the Jackal is providing him with. They are suddenly attacked by the Punisher. Spidey's spider-sense goes off, warning him that the Punisher has them in his crosshairs. The Punisher fires his gun; the bullets meant for Spidey. The Jackal leaps in front of Spidey, taking two gunshots to the chest; he falls to the ground. As he lies dying on the ground, the Jackal tells Spidey that the answer is in his bloodstream. But before the Jackal can continue with his explanations, the Punisher arrives to finish the job. Spidey attacks the Punisher and easily knocks him out. He then grabs hold of the Jackal and races back to the Jackal's lab where he puts him inside a cellular regeneration pod to heal his wound before it is too late. As Spidey sits next to the pod and eagerly waits for the results, the Jackal thinks to himself that things could not have worked better if he had planned them himself.

In Amazing Spider-Man #404, Part Three of Six of the Maximum Clonage storyline, Spider-Man is still waiting outside the cellular regeneration pod inside which the Jackal is recuperating from his wounds sustained in the previous issue, when the Scarlet Spider, arrives on the scene, having finally tracked him down. Ben tries to comfort Peter but Peter lashes out at him. Ben continues to try and reason with Peter but Peter wants to be left alone and walks away. Just then, Spidercide appears and he is not please to see Ben at all. As this takes place, Kaine watches from above, and decides to let Ben die once and for all. Kaine turns his attention to the regeneration pod that contains the Jackal and destroys it. He pulls the Jackal out of the pod and asks him why he would take everything away from Peter especially since Peter has gone well beyond the Jackal's dreams of what a clone could accomplish. The Jackal offers Kaine a chance to be whole again, if he can figure out an end to the degeneration that is affecting him.

Peter/Spider-Man comes back and finds himself in the middle of the battle between Spidercide and the Scarlet Spider. Though Peter hates Ben, he does not know if he wants to see him die. The Jackal and Kaine also return. Ben continues to try and reason with Peter but Peter appears to be involved too much with the Jackal's schemes. Ben lashes out at the Jackal but both Peter and Kaine stop him, telling him that he does not belong in their world. Peter tells Ben to go back and claim his life and to leave them all alone.

While this discussion takes place, Spidercide is compelled to go down an empty hall, where he finds the source of the power calling for him: Scrier. Scrier is now revealed to be an entity, whose purpose, if revealed, would be unfathomable to the mortal mind. Spidercide asks Scrier to reveal himself to him. With the touch of a finger, Spidercide learns all and goes back to the main room where the Jackal orders him to kill Kaine. In Spider-Man Volume 1 #61, Part Four of Six of the Maximum Clonage storyline, the Scarlet Spider decides to run away rather than face the hundreds of Spider-Man clones racing towards him. His main objective is to find Peter to try and reason with him regarding his alliance with the Jackal, who is now telling Peter to bring back the original Gwen Stacy clone. Ben continues to search for Peter and he is being hunted by the Spider-Man clones, who have spread out through the Jackal's lab to try and find him. Luckily for Ben, it means that he only has to fight five or six of them at one time instead of a few hundreds.

In New York City, at the Parker home, Kaine confronts Mary Jane to try to figure out why Peter gave up his life to be with the Jackal. MJ has no clue whatsoever and asks Kaine why he cares so much. With that, Kaine reveals his full origin to her. He explains about the day he emerged from a cloning pod and how Professor Miles Warren was so pleased with the results until a small scar developed on his face. Though the scar was small, it was enough to distinguish him from the real Peter Parker, so he was cast aside. He continues explaining how he ran off before Professor Warren could dispose of him. He stayed close, however, lurking in the shadows, since it was the only life that he knew. He watched as Peter, his brother, emerged from the same cloning pod, and went on to live the life he could never have, to be the hero, the man that Kaine could never be and a symbol for him that he loved. Mary Jane tells Kaine that he is alive, no matter how he was born and she tells him to do what Peter would do, which is to accept the responsibility, just as he has accepted the powers.

Elsewhere, Peter Parker finds the Gwen Stacy clone, who had been expecting him. Together, they swing back to the Jackal's lair. Meanwhile, at said lair, Ben is still fighting off the hundreds of Spider-Man clones, when he discovers where the Jackal's new lair actually is: the old smokestack where his supposedly dead body was left (back in Amazing Spider-Man #149-151). Ben could spend days dwelling on it but the unexpected arrival of the entire army of clones quickly takes him back to reality. Within seconds, Ben is cornered by the clones. But, as they gang up on him, someone distracts them: Kaine. Ben tells Kaine that he will not stand by and let him kill the clones. Kaine agrees to not kill them, saying that they have as much right to live as anyone.

In Spectacular Spider-Man #227, Part Five of Six of the Maximum Clonage storyline, Ben Reilly, as the Scarlet Spider, and Kaine continue to battle the hundreds of Spider-Man clones.

Meanwhile at the Parker apartment, Mary Jane gathers all of Peter's spider-tracers and activates them all at once in order to summon him. Miles away, Peter, accompanied by the Gwen Stacy clone, receives the signal and races back to the apartment, Gwen in tow.

In another part of the city, the Jackal expresses his concerns about the lone survivor of the mass genocide of Springville, Pennsylvania to Spidercide, his disciple. The Jackal simply cannot understand how that man survived his new and improved Carrion virus.

As Kaine and Ben continue battling the Spider-Man clones, they come to the realization that the clones were taken out of the cloning pods too early when they start decomposing in front of their eyes. While Kaine increases the pace of the fight, Ben tries to convince the clones that they can have normal lives if they try, citing Peter Parker as an example. Speaking of the devil, Peter arrives at the Parker apartment with Gwen and Mary Jane and Gwen quickly bond.

Ben tries to refrain from defending himself against the numerous attacks of the Spider-Man clones but Kaine does not. Several clones are sent crashing through a skylight and into the Jackal's lair. Witnessing this, the Jackal calls Spidercide to his side but the latter is nowhere to be found. Just then, Kaine enters the lair through the same skylight so the Jackal runs away to find his seemingly faithful clone (Side note: the New Warriors' top priority is to find the mastermind behind the destruction of the town of Springville). The Jackal catches Spidercide in the process of copying all of his files on the Carrion virus and sending them via modem to Scrier. He snaps his fingers, trusting that it will cause Spidercide to destruct on command (as it did for so many others) but it surprisingly does not work and Spidercide punches him across the lab, telling him that his degeneration factor was removed by Scrier in exchange for information. As Spidercide prepares to kill the Jackal, Kaine storms in and stops him. While all this takes place, Ben continues to fend off the attacks of the many Spider-Man clones who are started to degenerate even more in front of his eyes, causing him to puke on the ground.

Kaine and Spidercide engage into a fierce but even battle. However, when Kaine becomes distracted by another vision of Mary Jane dying, Spidercide impales him using a large piece of metal. At that exact moment, Ben arrives and takes on Spidercide while the Jackal grabs hold of Kaine and puts his body inside a regeneration pod before taking his leave. Ben gets the upper hand on Spidercide and sends him crashing into some kind of electrical apparatus, seemingly killing him. This results in a power outage in the whole building, allowing the sole survivor of the Springville genocide to escape. At issue's end, Ben confronts the Jackal but comes under attack by a large pile of genetic goo controlled by his opponent.

In Maximum Clonage: Omega, Part Six of Six of the Maximum Clonage storyline, Ben Reilly has his hands full with the creature that is made up of genetic tissue of all the decomposed Spider-Man clones. However, when the Jackal threatens to kill his friends at the Daily Bugle, Ben gets a surge of energy and determination and he manages to break free.

Meanwhile at the Parker home, Mary Jane implores Peter to stay home with her and their unborn child while the Gwen Stacy clone screws up with his head and tells him that he belongs with his fellow clones. Peter tells MJ that he does not deserve her or the baby and he takes off with Gwen and heads out to find the Jackal.

When they arrive at the Jackal's lair, they find nothing but booby traps left by the Jackal to keep intruders away. Using his trusty spider-sense, Peter gets through them and discovers the Jackal's plan for the Daily Bugle and the rest of the world. Meanwhile, back at the Parker apartment, MJ dredges up some of Peter's spare web cartridges to help him and Ben for whatever they may need.

The Jackal, meanwhile, is in the process of setting up a Carrion virus bomb at the Daily Bugle (on the rooftop), when Scrier appears and tells him to stop what he is doing, because the destruction of the human race cannot be allowed. Scrier then orders Spidercide, who survived his battle with the Scarlet Spider in Spectacular Spider-Man #227, to deal with the Jackal.

Just then, Ben (the Scarlet Spider) arrives on the scene and attacks the Jackal and Spidercide. As the battle rages on, the Jackal torments Ben by asking him if he will be able to save his friends at the Daily Bugle, as successfully as he saved the real Gwen Stacy (which he didn't). Hearing those words, Ben comes to the realization that the Jackal's hatred for Spider-Man stems from the fact that Professor Miles Warren, the Jackal's alter-ego, blames Spider-Man for the death of Gwen Stacy. Spidercide takes over the fight against the Jackal from Ben, giving the latter some time to rest. Ben does not have the opportunity to rest for very long, as he finds himself back in the mêlée just in time to witness as Spidercide prepares to deliver the final deathblow. However, in the ensuing confusion, Spidercide is sent falling to his death from the rooftop.

Now facing the Jackal, Ben tries to get him to reveal how he managed to get him (i.e. Ben) to believe that he was the clone for all those years. The Jackal confesses that he implanted the thought in his brain while he was taking cell samples for his clones. On cue, Peter, as Spider-Man, and the Gwen Stacy clone arrive. Ben tells Peter to handle the Jackal while he takes care of disposing of the Carrion virus bomb. Unfortunately, as Ben works at defusing the bomb, the Jackal and Peter unwillingly bring the fight to Ben, forcing him to join in. Peter and Ben manage to web up their common adversary, and then they go to dispose of the bomb before it explodes. Though they do manage to defuse the bomb, they have another problem on their hands: the Gwen Stacy clone has gotten herself a gun and is readying herself to shoot the Jackal. The Jackal breaks free from the webbing while Ben and Peter try to convince the Gwen-clone not to become a killer and Mary Jane arrives on the scene. Distracted by Ben and Peter, the Gwen-clone loses her gun and is knocked off the rooftop by the Jackal. The moment seemingly frozen in time, Mary Jane throws to Ben the spare web-shooter she grabbed earlier (why not Peter…I don't know) and Ben snags the Gwen-clone in mid-air. The Jackal is no so fortunate however, as he plunges after the Gwen-clone to save her, hoping to prove that he could do what Peter could not, and ends up falling to his death. His final words are: "When the dream ends, the nightmare begins".

Later that day at the offices of the Daily Bugle, Peter meets up with Robbie Robertson in the hopes of getting himself a photo assignment. However, because the building is being remodeled and Robbie is busy working on getting the paper out while the renovations are taking place, he does not have any time to find him an assignment. Disappointed, Peter takes off. As he walks along the street, he finds himself staring at a mannequin in a store window. As he continues to stare at it, the mannequin transforms into the Jackal. Realizing that he is hallucinating and totally freaked out about it, he changes to his Spider-Man costume and web-slings into the night. As he swings away, he wonders if the degeneration is what's causing him to hallucinate. What really scares Peter, however, is the thought that the Jackal is still messing with his head from beyond the grave. He is more determined than ever of finding out what is going on with him.

Meanwhile in another part of the city, Mary Jane Parker is in the midst of a modeling shoot for a new line of maternity wear. The agency she is working for seems to want to have her sign a long-term contract so that she could continue to model their designs throughout her pregnancy and beyond. Mary Jane overhears this and appears interested.

Several blocks south, Peter Parker, as Spider-Man, is contemplating calling on Ben Reilly’s friend, Seward Trainer, to help him identify what is causing the hallucinations he has been having. Suddenly, a powerful headache rips through his skull and sends him crashing onto a nearby rooftop. An image of the Jackal appears to him and explains that a genetic implant he put into his mind years ago has now been activated. The trigger words were "When the dream ends, the nightmare begins", which were the Jackal's last words when he fell off the side of the bridge in Maximum Clonage: Omega. And the command stemming from these trigger words is that Peter will now be driven to kill the person he loves most.

A short time later, Mary Jane returns home and finds Peter sitting in the living room. Grabbing tight onto his chair and holding himself back, Peter tells her to run because he has been programmed to kill her. He tells her to call either the Avengers or the Fantastic Four or anyone else that could stop him before he succeeds in his mission. Mary Jane grabs hold of a nearby lamp and smashes it on his head. She then takes off running.

The New Warriors are practicing their moves and combat skills against each other when they receive a call from Mary Jane, who is seeking the Scarlet Spider. Justice, their leader, picks up the phone. Terrified – she can see Spider-Man heading her way – MJ quickly explains the situation and asks to be told where they can meet them for assistance. She then makes her way aboard a subway train before Spidey can catch up to her. As she stands aboard the subway train, it is revealed that she did not call the Avengers or the Fantastic Four for fear that they would fight Spidey and possibly hurt him or maybe even kill him. She is confident that Ben Reilly and the New Warriors will be able to help.

Spider-Man eventually catches up to the subway train carrying Mary Jane. As he makes his way from one subway car rooftop to the next, Mary Jane also makes her way from one car to the other, having been alerted of his presence by fellow passengers. As the subway train comes to a stop at its next station, Mary Jane rushes out of it, thinking that she lost him. However, Spidey appears and grabs hold of her before she can escape any further. Just then, the New Warriors show up and tell him to back off and let the lady go. Spidey replies that he cannot and that he will fight them if they get in his way.

To be continued in Web of Spider-Man #129.