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.

Meanwhile at the Parker apartment, Mary Jane gathers all of Peter's spider-tracers and activates them all at once, hoping that they will give off a signal so powerful that Peter will not be able to ignore it. Miles away, Peter, as Spider-Man, is swinging above the rooftops with the Gwen Stacy clone in tow, when he feels the unbearable calling of the spider-tracers activated by MJ. The Gwen-clone asks what is wrong to which he replies that something must be wrong at home and that MJ must be trying to reach him. He is at first resilient to go over – he has not treated MJ very well over the last few days – but the Gwen clone convinces him to go.

The Jackal is perplexed as to why and how one man remained alive after being recently exposed to his new and improved Carrion virus, which he released in Springville, Pennsylvania (see Maximum Clonage: Alpha). He is even more confused as to why the virus seemingly gave the man the ability to instinctively recode his DNA in response to environmental conditions. Spidercide, who is standing by his side, asks the Jackal why he is so trouble by that single anomaly. The Jackal explains that one man in a small town of a few thousand people could conceivably translate to hundreds of thousands across the nation. That is something he will not and cannot tolerate.

The Scarlet Spider (a.k.a. Ben) and Kaine are still battling the hordes of clones coming at them when two of the clones tossed by Ben suddenly start to decompose. Figuring out that the Jackal must have taken the clones out of the lab before they were fully baked and that the fight is taking too much energy from them, Kaine drastically increases the pace of the fight by forcing them to jumpstart their degeneration process. To do so, he gives it all he's got, destroying clone after clone. Ben begs him to stop because what he is doing is practically killing them in cold blood. Ben even goes as far as trying to convince the clones to not fight them and telling them that they can live full and useful lives if they only give themselves the chance.

Peter, as Spider-Man, and the Gwen-clone, arrive at the Parker apartment and enter through the skylight. Mary Jane, who had been expecting only Peter, is completely taken aback when she sees the Gwen-clone. The Gwen-clone explains that she is indeed only a clone but does have fond memories of her. Mary Jane hugs her and welcomes her back. Gwen tells MJ that she is happy that Peter and her have finally gotten together.

Ben tries to restrain himself from fighting back the army of Spider-Man clones attacking him and Kaine but Kaine is not. He sends a dozen clones crashing through the skylight leading into the Jackal's lair. Seeing this, the Jackal calls for Spidercide but the latter is nowhere to be found. As Kaine comes crashing through the skylight in pursuit of the clones, the Jackal runs away to find his (seemingly) faithful clone.

Meanwhile, at the headquarters of the New Warriors, the New Warriors are aware that thousands of people were murdered in Springville, Pennsylvania. Their leader lets them know that the sole survivor of the virus has been abducted before he could make it back to Project Pegasus. He also informs them that he believes that the mastermind behind the team that stole the contagion isotope from Genetech is the same that destroyed the town of Springville; therefore, finding him is now their top priority.

Back at the Jackal's lair, the Jackal finds Spidercide in the process of copying all of his files on the Carrion virus and sending them to Scrier. The Jackal is amazed at Spidercide's betrayal and proceeds to snap his finger, which is suppose to cause him to destruct on command. This does not work however and Spidercide explains that Scrier removed his degeneration factor. Having said that, he punches the Jackal across the lab, telling him that Scrier asked him to tell him how much of a disappointment he has been to him. Spidercide then prepares to deliver the deathblow when Kaine shows up and stops him.

In another part of the Jackal's lair, Ben is trying to fend off the attacks of the many Spider-Man clones. As he battles them, he tries to convince them to save themselves, telling them that they can live normal lives just like Peter Parker. However, as he pulls the mask off one of them, revealing a faceless putty-like head, he comes to the realization that they are but mindless killing machines, as Kaine told him. As if on cue, several clones surrounding him also start to degenerate into a pile of genetic waste. Completely disgusted, Ben pulls his mask off and starts to barf.

Elsewhere, Kaine is battling Spidercide, yet he does not know why he saved the Jackal's life and wonders if perhaps he is trying to win the Jackal's approval, or at the very least, his acceptance. Suddenly, Kaine gets another vision of Mary Jane's death, though, this time, he makes out the identity of her killer (though he does not reveal who the killer is). This moment of distraction on his part allows Spidercide enough time to grab a nearby large piece of metal and impale Kaine with it. At that exact moment, Ben arrives and attacks Spidercide. As the fight moves to another room, the Jackal kneels down next to Kaine and asks him why he sacrificed himself for him. Drawing his last breath, Kaine responds that it did so because the Jackal gave him life. The Jackal deems Kaine's response pathetic but does think to put Kaine's body inside a regeneration pod before leaving.

In another part of the Jackal's lair, Ben and Spidercide are still going at it. Ben punches Spidercide with all his might, sending him crashing into some kind of electrical apparatus, seemingly killing him. This crash causes every electrical system in the Jackal's lair to short out, thus giving the sole survivor of the Springville genocide an opportunity to break free from his glass prison. As Ben frees himself from underneath a hunk of debris that fell on him, the Jackal appears to taunt him. After telling Ben that he has to run – because Spidercide recently informed him that there is another player in the game – the Jackal snaps his fingers causing a large pile of goo in a corner to come together and attack Ben. Ben, whose ankle was sprained when he was stuck underneath the pile of debris, is helpless.

To be continued in Maximum Clonage: Omega.