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.

Kaine is taken aback and confronts the Jackal about him promising to make him perfect. The Jackal replies that Kaine is nothing more than a walking heap of genetic trash and a complete waste of blood and hair. Hearing those words, Kaine breaks down, begging the Jackal to not abandon him again. But then, Kaine ultimately realizes he was a fool to ever trust the Jackal so he takes his leave, vowing to kill him another time. Spidercide grabs hold of Ben and takes him to a different room where he throws him in. When Ben regains consciousness, he sees an army of Spider-Man clones racing towards him.

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.

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.

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".

A short time later, Peter returns home to Mary Jane. MJ tells Peter that she wants to stay in New York and continue on with the life they had before the whole clone nonsense started. Across town, Ben Reilly grabs all of his stuff and heads out the door.

Back in real-time, Ben gets a frantic call from said Dr. Seward Trainer, imploring him to get out of the cabin. Trainer cannot give him any further details, for fear that "they" will find him. Ben runs out of the cabin, just before it explodes. Fearing for his friend's life, Ben returns to New York to try and find him. Ben, as the Scarlet Spider, does not find Steward, but he does find these strange machines that are tapping into Trainer's computer mainframe, and then attack him when he gets to close to them. The machine's tentacled arms grad the Scarlet Spidery and shock him to the point of unconsciousness. At issue's end, it is revealed that Seward is imprisoned somewhere and whoever has him captive possesses long tentacled arms reminiscent of the late Doctor Octopus.

While the above takes place, Peter Parker appears to be going through some kind of emotional rough patch, as he crushes a brick with his hands as he is talking to his wife Mary Jane. Elsewhere, the infamous Vulture is out hunting for a body from which to steal more youth from, because he is starting to return to being just a frail old man once again.

Peter Parker, as Spider-Man, is making his way home, returning from an errand run, when he gets a sudden flash of Mary Jane, either in trouble or dead, just like the nightmare he’s been having. Confused as to whether the images are a result of the clone degeneration or him losing his mind, he rushes home to MJ.

As Peter/Spider-Man swings across the city, he contemplates calling Dr. Seward Trainer to see if he can help. Before reaching a decision, a powerful headache suddenly rips through his skull, sending 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.

Mary Jane returns home from a modeling shoot and finds Peter sitting in the living room, seemingly waiting for her. 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. While on the run from Peter/Spider-Man, MJ calls the New Warriors, asking for the Scarlet Spider. When their leader reveals that he is not there, MJ quickly explains the situation and arranges to meet with them. 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.

Peter/Spidey takes off after her, trying to figure out where she is going. Soon enough, he finds out; she drove him to the old Parker House in Forest Hills. When Peter/Spidey walks inside the house, he finds MJ casually sitting on a chair in the living room, surrounded by pictures of his family. MJ tells him that she has faith in him and also forgives him if he cannot control the programming in his brain. She also tells him that she prefers dying in a house full of good memories, than anywhere else. Childhood memories start flooding into Peter's brain, until he breaks down in tears, ridding himself of the Jackal's programming. MJ grabs hold of Peter tightly, as the Scarlet Spider watches on from a distance (he was close by as backup, just in case MJ’s plan did not work).

Seward Trainer is in his office, trying to break the encryptions when he finds the female Doctor Octopus in cyberspace. She is as surprised to find him there as he is but does not have a lot of time to dwell on it when the Scarlet Spider shows up to rescue him. That is easier said than done, because the female Doc Ock is revealed to be a lot stronger than expected. In the midst of the battle, Seward asks her why she is doing this, to which she replies that she was taught to revere scientific research above human life itself. When Scarlet realizes that Seward knows her and asks him about her, she reveals that she is his daughter.

The Scarlet Spider is taken aback by the revelation that the new female Doctor Octopus is Seward's daughter Carolyn. Conversely, Carolyn is furious with her father because he seems to share a father-son bond with Ben (i.e. the Scarlet Spider), a bond she claims she never had with her father. Ben wants to keep Seward safe but Seward doesn't want to repeat the errors of his past and leave his daughter again. Ben makes an executive decision and decides to grab hold of Seward and take off, the female Doc Ock in tow. As they escape, Seward notices that Ben is using more wisecracks than usual when he speaks and he comments on it. Ben replies that he is just trying to pick up where he left off five years ago.

At the hospital, MJ is not improving. While Peter continuously checks up on her, Ben Reilly and Trainer await the arrival of the messenger. As they wonder where he is, Trainer receives a phone call from his daughter Carolyn, the female Doc Ock, who informs him that she has the antidote and that she will give it back to them in exchange for him (Seward). Trainer notifies Peter and Ben and reluctantly agrees to her deal, knowing the Spider-Men will be close behind.

After telling MJ about the recent development, Peter dons his Spider-Man costume and swings off into the night with Ben, as the Scarlet Spider, and Seward Trainer. They drop Seward off at the rendezvous point and hide on a nearby rooftop overlooking the area. When Trainer disappears inside a parked van, Spidey and the Scarlet Spider decide to make their move. But, when they open the doors to the van, they discover a trap door leading straight into water underneath the docks. Fashioning themselves swimming gear out of webbing, they dive in.

Inside an underwater base, the female Doc Ock "persuades" her father to reveal access codes to a new technology he devised to project actual living matter into virtual reality. While she uses the codes obtained from her father to collect information from his computer files, she is alerted that Spider-Man and the Scarlet Spider have entered their hideout; her mysterious computerized ally sends a welcoming committee to greet them. Spidey and the Scarlet Spider fend off Doc Ock's goons and proceed in their search of the antidote and Seward respectively. Spidey finds the antidote, only to be attacked by the female Doc Ock. In another part of the underwater base, the Scarlet Spider finds Trainer but also comes under attack from the computerized entity, now revealed to be more than just a machine.

The battle between Spider-Man and the female Doc Ock takes an unexpected turn when Spidey causes the ceiling of the underground base to collapse and Doc Ock is swept away in the resulting undertow. Trapped underneath a huge pile of debris, Spidey is helpless. Elsewhere, the Scarlet Spider manages to short-circuit the electrical system, which forces the computerized entity to shut down. He then proceeds to free his friend and the two make their way out of there.

The Scarlet Spider enters the warehouse through the sewer system and starts looking for Detective Raven. Making his way through the warehouse, he ends up running into several more of the strange creatures that attacked Detective Raven. The creatures try to stop him but the Scarlet Spider takes them out and makes his way deeper inside the warehouse, where he finally locates Detective Raven, though Raven is trapped inside some kind of cocoon. The Scarlet Spider frees Raven only to be surrounded by more of the creatures, which have returned. As the Scarlet Spider readies himself to battle them, the High Evolutionary appears, telling the creatures, named Animen, to stand down. He starts to teleport them back to Wundagore, their home, but the Scarlet Spider tries to interfere with the teleportation. As he does so, he accidentally is transported to Wundagore, where he is quickly surrounded and outnumbered. Though he puts up a good fight, there are too many of them and he gets captured.

Another creature show up and recognizes the Scarlet Spider as "the other". The Animen are taken aback and bow in admiration. As the Scarlet Spider looks around, he sees a statue erected in memory of the Jackal. It is revealed that the Animen believe – as was revealed in Spectacular Spider-Man Annual #8 - that the Jackal infected his assistant Anthony Serba with a genetic virus that altered his DNA, turning him into a biological duplicate of the original Peter Parker. The Scarlet Spider tries to argue that it is not the truth, but the Animen call him a false prophet. The Animen go on explaining how the High Evolutionary wanted to create a new race by evolving animals into higher form and that it was thanks to Professor Miles Warren that they were able to do so. The major drawback, however, was that the High Evolutionary wanted to create a race of gods, while Professor Warren wanted to create the perfect human. As a result of this disagreement, Professor Warren was banished from Wundagore. Nonetheless, several "new men" followed him back and volunteered to undergo genetic experiments. Unfortunately, the experiments did not turn them into human; rather, they were turned into living corpses until their death: the Carrion virus.

It was around that time that Professor Warren started experimenting with cloning in order to create spontaneous life. In the guise of the Jackal, he returned to Wundagore to try and blend in with the creatures. He revealed to them that he perfected the cloning process and gained new followers as a result of this revelation. Angered by the Jackal's affirmation, the High Evolutionary took steps to prove that he was a fraud by capturing the Gwen Stacy clone and performing a series of tests on her; tests that revealed that she was not a clone at all – she is nothing more than a genetic duplicate. The Jackal's followers were not easily convinced and made arrangements to retrieve Professor Warren's journal. Reading through the journal, they discovered that the High Evolutionary was telling the truth.

The Scarlet Spider is taken aback by this surge of new information and as he thinks about it, the High Evolutionary teleports him to his "ready room". Then the High Evolutionary decides to tell him the whole story about Professor Warren and the clones. It is revealed that Warren was indeed his assistant and working on ways to turn animals into sentient bipeds. The jackal was the one creature Warren was enamored, however, the experiment turned out to be a failure – the jackal creature resulting from the experiment, seemed to exhibit a Jekyll and Hyde personality. Professor Warren was consequently banished, though the Jackal stayed in his life, hunting him and going so far as kill his family. Blaming the High Evolutionary for their deaths, Professor Warren returned to Wundagore to challenge him. Since his cloning process was a threat to the High Evolutionary, a false journal was planted in one of Professor Warren’s labs. This journal outlined a story about genetic duplication so Professor Warren's people would not know the truth and hold him with such reverence. Eventually, Professor Warren indeed perfected the cloning process, and the Gwen Stacy and Peter Parker clones were created and they were not genetic duplicates but the real thing.

The new female Doc Ock and her henchmen attack Mr. Tso to get hold of a chip needed to finalize the "merge" of the two worlds. Alastair Smythe, Tso's employer, sends his Cyber-Slayers after Ock and her cronies. However, before Smythe can revel in his victory, Mr. Tso double-crosses him and he takes control of the Cyber-Slayers, leaving Smythe to take on Doc Ock by himself. Though Mr. Tso momentarily gets away, he meets his demise when The Pro catches up to him.

Doc Ock's and the Master Programmer's plan to merge reality with Cyber-Space seems to come to fruition when reality begins to shift and the Master Programmer start to take on a more human form. Fortunately, the Scarlet Spider, assisted by Seward Trainer, uploads a computer virus into the system and it neutralizes the entire merging process. The Scarlet Spider saves the day, however Doc Ock manages to escape before he can stop her. Despite his heroic efforts, people still think the Scarlet Spider is a terrorist and monster.

As Spider-Man, Ben goes out for a swing and immediately finds trouble, in the form of a villain known as Armada. As Ben takes care of Armada, he is unaware that a woman named Jessica Carradine is snapping pictures of him and it is revealed that she has waited a long time for this day to come. Though Ben takes Armada into custody, he fails to apprehend some of her technical gadgets, which fly off with a revolutionary broadcasting chip that was stolen earlier in its possession. As Ben heads home, the gadgets return to their true master: Mysterio.

The following day, Ben, now with his hair died blond, goes back to the Daily Grind to repay the owner for the money she loaned him the previous night. Sensing goodness in his heart, the owner gives Ben a job as waiter. Later on that day, Ben returns to the cemetery to thank Aunt May and Uncle Ben for making him the person he is today.

When the Human Torch arrives at the statue, he finds Spidey being offered a freelance job with the Wild Pack by Silver Sable herself. After she is gone, Torch confronts him and berates him with tons of questions about who he is and what happened to the original Spidey. Ticked off, Torch flies off, vowing to keep an eye on him, calling him a "phony" in the process. Once everybody is gone, Ben thinks about how difficult things have become since he was last on active duty. He wonders what kind of world he's in, with the Human Torch as an enemy and the Sandman as an ally.

As Spidey is ensuring that no one was left in the buildings, one of the buildings suddenly comes crashing down and the female villain known as Poison emerges from the wreckage. Poison, who met Peter Parker that day, tells Ben that her son – who happens to be the boy he just saved – is in danger. As she is about to explain the whole situation to him, El Toro Negro, one of the contestants from the "Great Game", who was introduced in the Scarlet Spider books, attacks the ambulance carrying Poison's son Carlos.

Spidey meets with Randolph Hines, the president of the company that broadcasts Mystery Vision. Hines gives him a tour of the facility and lets him try some of the technology. Hines is then revealed to be Mysterio in disguise and reality starts to shift, creating confusion for the wall-crawler. He no longer knows what is real and what is an illusion. Spidey is actually unaware that he is wearing adhesive, film-like receivers over his mask, placed there when he was toying around with the technology, which causes him to see the illusions as real. Totally disoriented, Spidey tries to swing out of the building but his web-shooters malfunction, causing him to fall.

Ben Reilly is awakened the next day by Jessica Carradine, who is ready for their next date. As they walk along a street, they notice that people are assembled in front of an electronics store and their eyes are glued to a television set on display behind the window. Just then, a nearby traveling truck loses control and crashes. As Ben wonders how he will be able to change into Spider-Man, with Jessica standing next to him, and help the truck occupants, Jessica takes off running towards the accident to take some pictures to sell to the Daily Bugle. Ben uses the opportunity to slip away and transform into his alter ego. He then races back towards the truck to help the driver and passenger. As he pulls them out of the wreckage, he notices that Jessica is focusing on him, snapping his picture, and causing him to be worried. Jessica suddenly stops taking pictures when she gets caught up in the excitement over the television set on display and becomes somewhat of a zombie herself. Once Spidey drops the accident victims off to safety, he proceeds to cover up the television set, thus freeing its viewers from its influence.

With some assistance from Dr. Ramirez, Spidey reverses the signal of the lenses that were place over his mask and manages to locate Mysterio's new digs. He heads over there to confront the master of illusions. After breaking in the facility, he is confronted by various illusions, but battles through each one, using his trusty spider-sense as a guide. At issue’s end, Spidey destroys the device that forces people to watch Mystery Vision and captures Mysterio.

Elsewhere, the Rhino catches up to Kaine and Shannon Fitzpatrick. The ensuing battle is soon "crashed" by two contestants of the "Great Game", Joystick and Polestar. Ticked off, the Rhino focuses his energy on destroying them, rather than continuing to beat on Kaine and Shannon. Swinging nearby, Spider-Man decides to intervenes, before the entire city is demolished and innocents are hurt. During the battle, Kaine gets the upper hand on the Rhino and manages to slip away with Shannon, but not before Shannon is able to place a call to Johnsmeyer, whom she has been allied with all along. At issue's end, Carolyn Trainer, the female Doctor Octopus pays a visit to her father, Dr. Seward Trainer, at the hospital, and tells him that he will soon pass on.

During the drive home, Ben tells Peter about the concerns he has with his new girlfriend, Jessica Carradine. He shows him a picture of Jessica on her 7th birthday, with a blurred image of her father in the background, and tells him that there is some kind of connection between her father and her hatred towards Spider-Man. Ben goes on explaining how she was upset when he reacted strangely upon finding out about her over-the-top fascination with Spider-Man, as displayed by the wallpapered room of Spider-Man photos. It was then that she asked him to trust her and proceeded to reveal that her father was sent to prison for a crime he did not commit. Jessica had then explained that her father was accused of murder but the truth was, an old man had mistaken him for a burglar, had pulled a gun on him and in the ensuing struggle, the old man was killed and her father was found guilty and sent to prison. When he – Ben – had tried to figure out how Spider-Man was connected to the story, Jessica had simply kept going on and on about how Spider-Man was a murderer. Trying to defend Spider-Man, Ben had asked her if her father had ever interacted with Spider-Man. Jessica remained evasive and told him she did not like to talk about it. Ben then tells Peter that, after stopping by the Daily Grind to drop off his time card, he ran into a victim of an attack by someone who sounded suspiciously like Carnage. This led him to come to Ravencroft to verify that Carnage was still in custody, which is when the authorities showed up and Peter arrived shortly thereafter to help.

Ben Reilly, as Spider-Man, is now following John Jameson, head of security at Ravencroft. His hunch proves fruitful when Jameson transforms into Carnage. Ben confronts Jameson/Carnage to find out how the symbiote bonded to him and to help him get rid of it. Jameson manages to fight off the symbiote’s influence just long enough to tell Spidey that the symbiote is using him as a temporary host until it finds someone with more strength. Just then, the symbiote launches itself at Ben/Spidey, bonding with him. The Spider-Carnage immediately starts to cause mayhem throughout the city, followed by Jessica Carradine, who is snapping away with her camera.

While Spider-Carnage waits for Peter Parker, the alien symbiote in him tries to take over Ben's conscience. It suggests to him that he ought to kill Peter so there would be no question as to which one, out of the two of them, is the clone. Ben manages to control the symbiote and not kill Peter, who has arrived. However, Ben's internal struggle strikes a chord with Peter, who suggests that they ought to visit Dr. Seward Trainer to try and get some answers. Somehow infuriated by Peter’s suggestion, Ben lashes out at him and forces him to leave his apartment.

While this takes place, Peter Parker is busy tracking down Dr. Seward Trainer's whereabouts, which lead him to the Multivex Corporation. He tries in vain to obtain some information but is escorted outside by security. As Peter takes his leave, a mysterious person inside the building tells Trainer that they wish to see him continue his experiments in private. The purpose of the experiments is not revealed.