Act One
Peter Parker (aka Spider-Man) has recently been having black outs, dizzy spells, and enigmatic dreams, which includes
Morlun,
Kraven the Hunter, frogs,
Uncle Ben, and spidery imagery. In confronting a new villain calling himself
Tracer who is robbing a bank, Spider-Man suffers a bullet wound to the shoulder. Tracer escapes, while Peter goes to see Dr. Castillo, a doctor recommended to him by
Captain America, who treats Peter's wound and takes a blood test. Dr. Castillo later informs Peter that he is dying, which Peter relates to his wife,
Mary Jane Watson-Parker.
Later, May Parker, who wakes up from a strange dream and, after being yelled at by an emotional Peter, goes to the kitchen and finds Tracer. Tracer tells her that he is a reserve Avenger who is there to watch over her. During their conversation, he tells May that he is a machine god; in the same way that humans created gods, machines created him.
Meanwhile, Spider-Man is fighting Tracer's robot followers in the city when his powers start to fail. Morlun confronts him and tells Peter that he would rather watch Peter deteriorate than fight him. Spider-Man returns home and, finding Tracer, attacks him. However, Tracer assesses his health and refuses to fight him in his current state. Peter becomes enraged at Tracer's nonchalant attitude about his plans to kill Aunt May, and strangles Tracer to death. His skin melts away to reveal a machine body. After this, Peter tells Aunt May what is wrong with him.
Act Two
Peter goes to see
Mister Fantastic, who tells him that his condition is not caused by cancer or a viral or bacterial infectious disease. He is informed by
Yellowjacket that the illness was caused by a radiation-based infectious disease. Peter goes to see
Bruce Banner, an expert on radiation-based mutation. Banner tells Peter that at the rate the infection is spreading, a cure could not be developed in time to do any good. Peter then sees the
Black Panther (who had mapped the
human genome fifty years before
Western scientists) on Banner's suggestion, but he also cannot find the source of Peter's illness. Back in
New York, Peter encounters "The Ox" and, thinking him to be Morlun, fights him. In his anger, Peter almost kills him before
Daredevil stops him. Later, Peter goes to
Doctor Strange, who tells him he cannot use his magic to cure Peter and tells Peter to prepare himself for death.
Peter,
Mary Jane and
Aunt May go to Latveria to use Dr. Doom's Time Machine to see past scenes in his life, like the day Richard Parker and Mary Fitzpatrick-Parker left Peter in the care of his Uncle Ben and Aunt May. After returning to Stark Tower, Peter plans a trip to
Las Vegas with Mary Jane, namely in Tony Stark's penthouse suite. As he thinks of what it would be like in Las Vegas, Peter thinks about using his
spider-sense to win at blackjack, in the hopes of making enough money for his family after he is gone, but of course, even Vegas would most likely be hit by super villains he would have to fight. In New York, Morlun is looking for Spider-Man, in vain, as Peter and Mary-Jane are in one of Stark's space pods, looking down upon the Earth.
Later, Peter tries to clear his head with web slinging. Not expecting to be attacked, Morlun takes Peter off-guard and a fight ensues that sends Spider-Man flying through J. Jonah Jameson's office. Spider-Man then moves the fight away from civilians and to Empire State University, where he was bitten by the spider that gave him his powers. The fight intensifies as momentum swings from Morlun's side to Spider-Man's side. After an exhausting array of punches and kicks, Spider-Man starts to think that he has the victory after a titanic and epic duel that raged across the city. However, an unscathed Morlun plucks Spider-Man's left eye out and devours it. Morlun then savagely beats Spider-Man into a bloody, unconscious mess.
Act Three
Before Morlun can kill Spider-Man, the police show up and Morlun leaves Spider-Man's bloody, unconscious body, planning to finally drain his life force when the hero is alone. The
paramedics take the near-dead Spider-Man to the
hospital, with the
Avengers and
Mary Jane Watson on the way as well when they hear what happened on television, and they learn that Spider-Man's injuries are too severe. Morlun goes to the unconscious Spider-Man's hospital bed to finish him off, but MJ attempts to stop Morlun, who effortlessly throws her across the room and also breaks her arm. Peter suddenly wakes up, and using the last of his strength, the savage, animalistic spider-side of himself takes over (granting him sharp teeth and stingers in his wrists), and he attacks Morlun, pinning the villain and impaling his arms to the floor. Peter then bites into Morlun's neck, killing him. Reverting to normal, Peter says goodbye to MJ and falls to the floor, seemingly dead. As Aunt May and Mary Jane break down over the news,
Iron Man takes Spider-Man's body, so that the public will not know that Spider-Man is dead.
Spider-Man is thought to be dead, and Iron Man transports his body away from the hospital. Mary Jane, Aunt May, and Jarvis, Iron Man's butler, meet together to grieve over Spider-Man's/Peter's death. After inspecting the body, Mary Jane talks to both Captain America and Iron Man over how to divulge the secret identity of Spider-Man. Later Wolverine flirts with MJ but to no avail as Mary Jane conceives it as another one of Wolverine's attempts to seduce her into an affair; it turns out that Wolverine only did so in an attempt to deflect her mind from the loss of her husband. After being unable to sleep, Mary Jane has a conversation with another New Avengers member,
Spider-Woman (Jessica Drew), who tells her that her own and Peter's powers both derived from the spider, and that she could sense when Peter was going down; this obviously is through the mystical side of their powers. Both Spider-Woman and Spider-Man got their powers via radiation involving some form of spider DNA, and thus their powers are extremely similar. In the middle of the talk, there is an audible crash from the chamber where Peter Parker's body is kept. Mary Jane and the New Avengers arrive at the scene, to find that Peter's body has been hollowed out. Judging by the amount of glass outside the window, Captain America judges that the intruder escaped but not entered through the window. Mary Jane discovers the secret: all that is left is a skin. The scene cuts to a teacher explaining about spiders to her class and how a few rare species can shed their skin and begin anew. As the class goes to leave, we see a cocoon of webbing fastened to the Brooklyn Bridge.
Several days have passed since Peter shed his skin and begins with Iron Man flying around searching for him. Under the Brooklyn Bridge, Peter sleeps inside his cocoon and has a strange dream. A voice tells him he never understood what he was, accusing him of being too scared to truly be a "Spider-Man", only focusing on the human part and neglecting the spider part. Morlun managed to kill the human part of Peter, but the spider in him survived and killed Morlun, saving them both. The voice tells him that he will only be reborn if he accepts both parts, and warns him that Peter could be reborn very differently. Peter's soul agrees and is reborn, outwardly human. He goes to the Avengers Tower and swears to Mary Jane and Aunt May that he will never leave them again. Later in the night, Peter goes to the lab where his husk is and recalls the final warning of the voice: "Are you the man who dreamed of being a spider? Or the spider who dreamed of being a man? Are you the one...or are you
the other?" Shaking off the warning, Peter removes the wedding ring from the husk and heads back to bed.
Act Four
Peter gets a check up from Stark. As it turns out, Peter's wounds from his old enemies have been healed, including his missing left eye, and even the tonsils he lost in fourth grade have reappeared. As Stark puts it, Peter's "odometer had been reset" (this would be the first time he had an
exoskeleton processed). Before the test could continue, Aunt May stopped it and told Peter to "go play." So Peter and Mary Jane go out and swing throughout the city, talking about how they feel about the recent events that have occurred. Meanwhile, in Stark Tower,
pirate spiders have started to eat Peter's old dead body. When Spider-Man returns, he finds the top of Stark Tower covered in webbing. Inside the tower, Spider-Man finds the pirate spiders with Peter's old body. Using Peter's skin as a base, they have formed a body of their own. Engaging in battle, Spider-Man finds that the stingers he used to fight Morlun appear once again, but he is confused because "Spiders don't have stingers!" Before anything else can happen, the pirate Spider punches through the walls of Stark Tower and runs off. Spider-Man chases it down, but then it heads into the sewer. It forms a cocoon in a church. Spider-Man tells the New Avengers he has no idea about it and they want to run some more tests on him.
In a
subplot,
Flash Thompson, awakened from a coma, attempts to get a job at the school where Peter teaches. He is missing some memories, as he still calls Peter "puny Parker" and says that he hasn't seen him since high school.
Peter follows the otherworldly being (who may be “The Other”), only for it to inform him that they are both parts of the same whole, that spider-based cosmic forces are vying for control of his life and that she (the being possesses recognizably female build) is his opposite. Apparently, although a spider-deity known as “The Great Weaver” (also seen and mentioned in
Araña: The Heart of the Spider) thought that Spidey’s death was premature and pulled him back from his fate, others disagreed – and Peter feels his life being pulled in different directions as a result, at the center of a metaphorical spider’s web where he is unsure if he is the predator or the prey.

The "Iron Spider" costume. Art by
Michael Turner.
Peter is still in a state of confusion and is having some sort of an identity crisis after his rebirth. With no time to contemplate the events of days past, Spider-Man rushes to the scene of an explosion where a building was just demolished and people are trapped under the debris. Spider-Man quickly begins to "dig" into the remains of the building, and in his attempt to find survivors, he discovers that his soul was imbued new powers from the dream, including night vision, the ability to feel vibrations through his webbing, and the ability to adhere to objects via the skin on his back, allowing him to securely carry items such as the small girl he found and rescued.
Spider-Man successfully rescues a few survivors and learns that his new powers have appeared because he is now "embracing the Other." Peter then returns home to be with Mary Jane, and they watch the nightly news which portrays Spider-Man as a hero. The issue and this storyline conclude with Tony Stark beginning work on a new costume for Spider-Man.