The film begins with a flashback of Richard in his lab at Oscorp destroying his work. He kills various cross-species spiders in glass cases. He then leaves Oscorp, ransacks his own home (going into the basement to record something for his Roosevelt project) and then drops Peter off at Ben and May's as seen in the first film. We then see Richard and Mary on a plane, Richard is talking to May about how their lives are never going to be the same. Richard is uploading his work to a server elsewhere via laptop, a man then walks out of the plane cabin with blood on his hands. Richard notices this and asks if he can speak to the pilot, this results in the man pulling a gun and shooting May. Richard gets the gun off of the man and shoots a window, causing the plane to fall apart. The plane dives to the ground as Richard watches Mary. Cut to black...
Spider-Man is skydiving, in pursuit of Aleksei and his thugs who are trying to steal an Oscorp truck that is carrying plutonium. Aleksei knocks a car out of the way, Spider-Man swings to save the person that the car is going to hit... it's Max Dillon. Spider-Man tells Max that he's his eyes and ears and then returns to pursue Aleksei. In the middle of the chase, Gwen rings Peter, telling him that he's going to be late for graduation. Mid-call, Peter sees Captain Stacy in a police cruiser, though this is just a hallucination. Peter tells her he's on his way, manages to stop Aleksei and races to graduation, even though Gwen has already given her graduation speech.
Peter sees Captain Stacy again at graduation but shakes it off. Gwen invites Peter to dinner, Peter realises that he made a huge mistake by going again Captain Stacy's wishes and is clearly distraught by this, resulting in Peter breaking up with Gwen. Though Gwen asserts that she breaks up with him. Some time after the breakup, Peter watches Gwen from afar as Spider-Man.
Harry Osborn is brought to Osborn manor, where he faces a dying Norman. Norman tells him that the disease that he is suffering from is hereditary and that Harry will soon share the same fate. Norman dies shortly after, resulting in Harry taking Norman's place as head of Oscorp, much to Donald Menken's disapproval. At a board meeting, Harry tells everybody on that table now works for Norman's assistant, Felicia, as she works for him.
Later on, Max is stuck in Oscorp on his birthday, Smythe allows everybody to leave apart from Max, he asks Max to fix an electrical fault. Max can't get in touch with somebody who's supposed to assist him and opts to do it himself. He electrocutes himself and falls into a tank full of eels. We now see Max in a morgue in a concrete cocoon of sorts, he jerks around and falls, the cocoon breaks up and his glowing skin shines through.
Max takes out a hoodie from a bin in the morgue and makes his way to Times Square, as he is thirsting for electricity. Max can see electricity glowing through walls and bags. From cables underground to phones in people's bags. Max attempts to drain all of Times Square's power from an underground generator but is stopped by a police officer. Meanwhile, Gwen and Peter have their first meeting in quite some time. Peter tells Gwen that he has been watching her for quite some time. Gwen tells him that she may possibly be going to England, to attend Oxford, before the two can continue, Peter's spider sense goes off and he leaves to go to Times Square. Spider-Man shows up and confronts Max, telling him to calm down so they can talk elsewhere. Max asks Spider-Man if he remembers him, Spider-Man barely does. A hidden sniper shoots Max and sets Max off on a rampage. Spider-Man subdues Max by dousing him with water from a fire hose.
Electro is now in Ravencroft, being experimented on by Dr. Kafka. Electro tells Kafka that soon everyone in the city will know how it feels to live in his world and calls himself Electro. We now move on to Peter, Peter is in his room looking at his now destroyed webshooter. Peter attempts to fix this in the garage before getting a call from Harry, who lets him know that he is dying. Peter goes over to Harry's, Harry tells him that he knows that Peter can get Spider-Man to meet Harry so that Spider-Man can give him his blood. Harry has worked out that Spider-Man is somehow cross-species and can self-heal. Peter refuses and leaves.
Peter is now at home, he finds himself coming back to his father's briefcase over and over again. He then decides to investigate his parents' death further, sprawling out a wall full of newspaper clippings, a map and thread, identifying ties between stories and whatnot. He then confronts May about the truth about his parents, May tells him that Richard and May was a suspected traitor and that he only cared about the money. She tells him that even she found it hard to believe as he would get the D train everyday like anybody else.
Later on, in a fit of rage, Peter tears down clippings from his wall and smashes a calculator from Richard's briefcase on the wall, it contains a number of coins/tokens, all identical. Peter investigates Roosevelt further online and ties it in with the D train, working out that Roosevelt had his own secret subway system. Peter ventures out to find this from online research, inserts a token from Richard's case into a booth, resulting in an underground train carriage to rise from the ground. The carriage contains Richard's work. A computer in the train automatically plays a video recording of Richard. Richard speaks about how Norman planned to sell his work to a foreign military buyer and when he refused, falsified information to paint Richard and May as traitors and frauds. Richard goes on to state that he anticipated something like this and as a result, used his own DNA in his cross-species work. So that only his bloodline could correctly integrate with cross-species work, acting as the missing jigsaw piece.
Peter decides to meet Harry as Spider-Man, he refuses to give Harry his blood and leaves a now enraged Harry. Peter catches up with Gwen who is on her way to her final Oxford interview, she tells him that the two are on different paths. He wishes her good luck and leaves. Meanwhile at Oscorp, Felicia tells Harry that there are hidden, secret Oscorp projects that not many people know about. Harry attempts to research these and finds footage of Max's accident amongst various project information. His access is revoked and Menken confronts him with guards. Menken plants information to make it seem as though Harry approved the cover-up of Max's accident, even though Menken did this. Harry is arrested and taken to Ravencroft. Harry takes down two guards and finds Electro, telling him that the two need each other. Harry promises to give him access to Oscorp's new grid, allowing him to have all the city's power. Electro agrees and breaks out of Ravencroft, the two then go to Oscorp.
Harry confronts Menken and asks him to take him to the underground project sector at gunpoint. Menken is forced to find the cross-species spiders, he tells Harry that even though the spiders were killed, their venom was kept so that research could be continued some day. Harry forces Menken to inject him with the venom, he does and Harry falls to the ground in pain. Menken escapes. Harry tears his shirt off, his skin is becoming scaley, patchy. His hands are claws. Still on the ground, he manages to enter a chamber containing a self-healing suit, it contains a glider. The suit detects his injuries and begins healing him. Now integrated with the suit, Harry is alone in Oscorp.
Gwen is on her way to the airport by taxi, she is held up by a traffic jam and leaves the taxi. She sees a giant "I LOVE YOU" sign made out of webbing on the side of the George Washington bridge. She smiles and Spider-Man swoops her away. The two are at the top of a bridge, Peter tells her that she is his path and that he will move to England with her. Flickering lights from Oscorp's power plant catch their eye. Peter suspects that it's Electro, he tells Gwen that he can't get close to him without his webshooters frying. Gwen tells him that magnetizing his webshooters will fix this problem. She does this for him with a car battery, he webs her to the hood of the car and leaves to go to the plant. He finds Electro and the two battle. Whilst Peter and Electro are battling, two planes in the sky are on a collision course with each other due to electrical interference. Peter temporarily takes down Electro and Gwen shows up, telling him that he needs her as she knows how to reboot the system. He tells her to go into the control room and wait for the go-ahead. Peter sees Captain Stacy's ghost one final time before Electro and Spider-Man battle. Peter tells Gwen to reboot the system and Electro is overcharged with electricity, he blows up, leaving behind the voltmeter that was on the side of his head. The two planes' navigation systems come back online and they just narrowly miss one another.
Peter and Gwen are about to leave as Harry, now as the Goblin, shows up. Harry looks at Gwen and works out that Peter and Spider-Man are the same person. He grabs Gwen and takes her to a nearby clocktower, he drops her from the top. Peter catches her and the two land on a walkway. Harry throws a bomb next to them and the walkway is destroyed. Peter lands on a gear and catches Gwen with a webline and reels her up. Goblin swoops in and attacks Peter, Peter battles Goblin whilst still holding the webline. Moving gears are about to cut the webline that Peter and Gwen are holding, he sticks his foot in the middle of the gear to stop it. He fails, the line snaps and he quickly knocks Harry out before diving after Gwen. Peter shoots a webline out to catch Gwen, the webline catches her waist and the sudden jolt from the stop causes her to hit her head on the ground. Spider-Man jumps to the bottom of the clocktower to see Gwen, he holds her, her nose bleeds and he realises what has happened. He hugs her and cries. Peter is now at Gwen's funeral, then at her grave. Peter visits her every day.
We are now in Ravencroft, where the Man in the Shadows visits a now visibly better Harry. Harry tells him that his condition comes and goes. The Man asks him how many people he wants for the project, Harry says he wants to keep it small, so six. The Man is identified as Mr. Fiers and goes to the underground sector of Oscorp with various hidden projects, walking past a harness with four mechanical tentacles, a winged flight suit and a mechanical Rhino suit. The Man speaks about the ideal first candidate, Aleksei Sytsevich. Peter is now in his room watching Gwen's graduation speech, he then hears about Aleksei breaking out of prison. Aleksei is wreaking havoc in his new mechanical suit, he yells and calls himself Rhino. A young boy (Jorge) dressed as Spider-Man who Spider-Man saved earlier sneaks under a barrier and confronts Rhino. Rhino moves closer and Spider-Man swoops in. Spider-Man thanks Jorge and tells him to look after his mother. Spider-Man jumps onto a car and talks to Rhino via megaphone. Rhino tells him that he is going to kill him. Spider-Man asks him if he wants him to come down so he can kill him, to which Rhino says yes. Spider-Man jumps off and Rhino charges on all-fours towards Spider-Man whilst shooting missiles at him. Spider-Man grabs a manhole cover and deflects the missiles. Spider-Man webs and swings the cover towards Rhino and as he slams it... we cut to black. End.
