Peter and Mary Jane are having lunch when they are visited by a very begrudging Steve Rogers, who tells Peter to suit up and meet him for training. Peter meets Rogers at the cemetery where they begin a lesson on fighting smart versus fighting foolishly and how the second one can lead soldiers right to a cemetery like the one they are standing in. Rogers gets called away by Carol Danvers, stating that General Nick Fury and his Avengers have gone rogue. Peter follows Rogers to the Queensborough Bridge where he witnesses a massive explosion.
Meanwhile, Norman Osborn once again transforms into the Green Goblin and escapes the Triskelion, along with Dr. Octopus, Sandman, Kraven the Hunter, Electro and Vulture and hides in an apartment building near Central Park. They witness the explosion on the news and Osborn states that since S.H.I.E.L.D. is occupied it's the perfect time to do God's work: kill Spider-Man. Otto objects to this plan and, although he is grateful that Norman freed him from prison, decides that he has no grudge against Peter Parker and wants to continue his career as a scientist, and tells Norman that they should be proud that they created Spider-Man together. Norman transforms and hurls Otto out of the window. Otto uses his ability to control metal to form his "Octopus Arms" out of any and all of the metallic objects in the area. Norman leaps after him, stating that Otto is a fool for believing that ever he had anything to do with the creation of Spider-Man after which Norman overpowers Otto and deals a fatal blow to him.
Peter gets a phone call from Mary Jane saying that Norman has escaped prison and will most likely come after Peter's family. He decides his family is more important than joining a fight he doesn't belong in and swings home before Norman and his crew can get there. Peter arrives at home and warns both Aunt May and Gwen to pack and drive away from the city until he calls them. He then heads out to find Norman to put an end to this, when he once again is called by Mary Jane. She tells him that she just witnessed Norman murdering Otto Octavius on the news. Peter heads to where the battle took place to find Otto's body lying lifeless in the middle of the street. A bystander points up to where Norman fled the scene to and Peter went to investigate the apartment above. Finding nothing there he once again heads out in search of Norman and the rest of his team of fugitives, when he spots Captain America standing over a beaten Nick Fury and decides to intervene. He arrives at the scene and sees the The Punisher aiming a rifle at Cap. He immediately dives towards Cap and pushes him out of the way, getting shot himself. Osborn and the remaining members of his group show up at the Tinkerer's Lair and demand he supply them with weapons, including Vulture's Suit as well as blasters and knives for Kraven.
Meanwhile back at the Queensboro bridge, a squad of S.H.I.E.L.D. Agents arrived at the bridge and, during the momentary confusion caused by Spider-Man's appearance, shoot and attempt to apprehend Fury. Filled with remorse, Frank begged the agents to "punish him" for shooting an innocent kid. Captain America promises Peter that his wound is not fatal and commends him for taking a bullet for him without a second thought, stating that when he grows up Peter will be the best out of all of them. War Machine then arrives and blows up the bridge, causing everyone but Spider-Man, who uses his ability to stick to surfaces, to fall into the water below. Peter manages to gain his composure and dresses his wounds with his webbing. He then decides he needs to go to a hospital, however doing so will require him to reveal his secret identity, which he decides he is fully prepared to do. He then spots Osborn and his crew and follow them to his house instead of going to the hospital.
Osborn and his group then appear at the Parker residence looking for Peter. However they are instead met by Johnny and Bobby. Johnny manages to overpower Norman, but Sandman intervenes and completely engulfs Johnny in sand, putting out his flame. Ice Man tries to help Johnny but is swiftly defeated by Electro. Just as they are about to enter Peter's house, they spot him down the street, unmasked. He quickly takes out the Vulture with his webs and, even though he can barely stand, prepares to fight the rest. Peter lies and tells the rest of the villains that S.H.I.E.L.D. and the New Ultimates are on their way, and that it would be in their best interest to just surrender. However Electro points out that Spider-Man is hurt and Sandman, Kraven and himself prepare to attack. Peter, thinking quickly, kicks open a fire hydrant and aims the jet of water at them using his hands. Electro shorts out and electrocutes both Sandman and Kraven. Peter then decks Electro, knocking him out. Peter then, exhausted, notices that a crowd of his neighbors has gathered around him in the street. Some of them are even recording him on their cellphones. He asks them to call the police and an ambulance.
Peter then gets attacked, once again, by Sandman, Vulture and Electro, leaving him even more injured than before. In a panic, one of the neighbors calls Aunt May and informs her that her nephew is Spider-Man and that he's about to be killed. May turns the car around and speeds back home. She arrives just as Electro is about to deal the final blow to Peter and manages to shoot him three times in the chest with her revolver. Electro falls to the ground, though to be dead, but not before once again shorting out and electrocuting Sandman and Vulture, leaving them all unconscious.
Mary grabs Peter and they embrace. Norman then wakes up and charges straight towards them.[7] Peter grabs hold of Mary and Gwen and swings them to safety. He then knocks Norman down long enough to wake Johnny up. Johnny lights up and confronts Norman, only to have Norman absorb his flame and knock Johnny to the ground. Empowered, Norman unleashes a storm of fireballs at Peter and the surrounding vehicles. In the fiery chaos Peter manages to flank Norman and hit him from behind with a mailbox and hurl him into the open jet of water from the fire hydrant he earlier used to take out the rest of Norman's group.
Stripped of his new power, Norman manages to once again get up and is about to deal a fatal blow to Peter when Mary Jane runs into him with a truck she managed to steal. The truck flips over but Peter manages to get her out and the two kiss. He then throws her to safety and, in one last effort, lifts the truck over his head and crushes Norman with it... twice. Unfortunately, before Peter is able to get to safety the truck explodes, critically wounding him, and hurdles him onto the grass. Mary Jane and Johnny (having woken up) rush towards him. MJ says they need to get him to a hospital. Johnny suggests that he fly him to the hospital, but MJ says he can't be moved in his current condition. Aunt May finally manages to get away from Gwen and back to the scene of the fight with Gwen chasing her, only for them to see Peter lying on the ground, dying. They immediately rush towards him, with Aunt May, asking him what he had done. He manages to tell Aunt May that he is happy that he finally was able to make up for not saving his Uncle Ben by now saving her. He then seemingly passes out and Johnny listens to his chest for a heartbeat, but to everyone's horror, hears none. In the fiery wreckage Norman, transformed back into his human form, manages to smugly smirk before he, too, dies.