While patrolling the city, Spider-Man angrily watches J. Jonah Jameson's newsflashes, spreading anti-Spider-Man propaganda. He swings through the city explaining to the audience that he isn't an ordinary teenager and asks why he can't get a little "spidey love". He quickly has to go to school, but along the way, he uses a web net to stop a police car with a sticky substance across the windshield. Trapster, a frequent villain the hero faces, was relying on this tactic to draw Spider-Man out in order to take him down. Spider-Man dodges his initial glue shots, but is adhered to the wall. He breaks free after shooting a web which causes Trapster's gun to malfunction and trap him with his own glue.
As Spider-Man is approaching the trapped Trapster, he notices that his enemy is scared but Spider-Man does not detect any danger with his Spider Sense, an "early warning system" that alerts him of danger. Spidey turns around to see the S.H.I.E.L.D. Helicarrier as well as Nick Fury who needs to talk to the hero.
The S.H.I.E.L.D. director commends Spider-Man for stopping Trapster but he points out that Captain America could have stopped the bad guy in less time with no collateral damage. Fury understands that every hero has to start somewhere, but eventually Spider-Man has to learn instead of being destructive. After Director Fury mentions Peter Parker's civilian identity and that he will turn him into the "Ultimate Spider-Man", Fury equips him with an automatic webshooter that will allow Spider-Man to aim more accurately, but Spider-Man denies the request.
After arriving at school, Mary Jane Watson finds Peter at his locker to show him a clip of J. Jonah Jameson's newscast against Spider-Man, saying that she wants to work for him in journalism someday. Next, he runs across his other friend Harry Osborn who has always been a good friend to him. He flashes back to remember the day he met Harry and Harry gave him a ride along with him and his father in their limo after Peter's bike broke in the rain. Soon, Peter's spidey sense goes off to alert him of Flash Thompson who is about to shut Peter in a locker. Stan the janitor lets Peter out and gives him a motivational speech on standing up for himself.
In the cafeteria, his spidey sense really goes off. Right behind him, an explosion goes off and the Frightful Four (minus Trapster) enter. They reveal that they know Spider-Man attends Midtown High. Wizard believes it could be anyone, so Klaw releases a sound blast to deafen everyone there. When Peter cries out against the villains trio, Thundra wants to crush him but Klaw emits a high-frequency noise at Peter. After getting free of the sound, Peter cries out for everyone to start a food fight to create a distraction long enough for him to change into his Spider-Man outfit. He is confused as to how the Frightful Four were able to find him, when he discovers a sensor stuck to his suit by Trapster.
Spider-Man begins fighting the villains, but Wizard transmits the battle to his boss, Octavius. As he talks to Norman Osborn, the millionaire orders him to abort the mission since his son Harry is at Midtown High. Using green jello, MJ is able to aid Spider-Man in taking out Thundra. Klaw blasts Harry and knocks him out. When Thundra again tries to charge the hero, he cocoons her in webbing. Attempting to use students as human shields, the Wizard is taken down by spidey from behind.
In the midst of battle, Flash asks to help Spider-Man, who he idolizes, but Peter, enacting some revenge, locks him in a locker. As soon as the police arrive, Thundra, Wizard, and Klaw flee the scene in order to avoid imprisonment.
After the incident, Harry is rushed to the hospital by his father. Peter sulks through the hallways saying this is his worst day ever.
Using this attack on the school as proof against the menace Spider-Man, Jameson issues more of his propaganda across the city. Back at home, Aunt May is worried about her nephew. Peter explains that he is able to use her busy schedule in order to sneak out for hero duty. Peter checks in on Harry at the hospital who is recuperating fine. Norman Osborn is suspicious of Spider-Man attending the boy's school. Peter forgot to pick up the cake after school in order to celebrate his uncle's birthday, but his aunt understands that he was under a lot of stress after the events that transpired at school.
In his room, he is smitten with guilt that he cannot become the "ultimate" Spider-Man without the proper help. He later goes out to town for Spidey patrol to find Director Fury. Using the S.H.I.E.L.D.-designed web shooter, he lands on the helicarrier where the security system tries to lose Spider-Man. Just before the guns can shoot down the hero, Nick Fury turns the system off and welcomes Spider-Man. Peter ends by saying "to be continued".