Peter Parker is an ordinary high school teenager who is waking up to go to school. We follow him going to school after having breakfast with his Uncle Ben and Aunt May. On the bus, he sits with Mary Jane Watson, a popular girl who hangs with him because they are good friends due to being neighbours most of them lives, and with Harry Osborn, who Peter tutored at first but has now become good friends with. We go through one regular day of high school for Peter, including him being bullied by Flash but tolerated by the rest of the popular group due to him being friends with MJ. We go to the next day where they go to the fateful field trip, where we learn about the spiders that have been designed to transfer certain spider attributes into humans, using a virus designed to change human DNA to be more spider like. However that virus isn't made active without a shot by the Neo-Genic Recombinator.
We see a spider being tested on in another room with the device. It is zapped, however it escapes as the students come in, going unnoticed until it latches onto Peter, biting him and causing him to feel immediately sick. The Oscorp scientists catch Peter's bite on video, but are not able to see the face of who it bites. The next day, Peter still doesn't feel the best as he goes to school. After bumping into Flash while going to class, Flash tries to fight him but Peter's reflexes kick in. He does not fight back, but is able to dodge all of his attacks. Peter eventually gets away from Flash. We go to his gym class when we see he is doing much better then normal, able to lift himself higher with his strength, run faster and longer around the course (etc, etc). The day ends and Peter goes to an abandoned building to see what's going on, where he tests out all his new powers (webbing not included).
The scientists at Oscorp are trying to find out who the spider bit, so they can bring him in for research. We see them building up schematics for Spider Slayers. The next day, Peter is feeling more confident then he did before at school, not being the typical shy guy he usually is. Peter goes home to start designing his costume, originally intended without a mask so he can show off how great he is now with all his powers. He finds a local obstacle course, with a 1000 dollar prize. Peter enters the race, getting a drive there by his Uncle Ben to save up his energy. Peter and Ben start to argue about how different Peter has been lately, acting more confident, especially since he hasn't been a sports guy before this.
Uncle Ben gives the famous line "With great power comes great responsibility". Peter leaves angrily, and wins the race. However the person running the contest doesn't feel that Peter won fairly, so he doesn't give him any money. Peter gets very angry and leaves, only for another contestant to come in and rob the building owner only for Peter to let him go. Uncle Ben is then killed by the robber like he was in the comics. Peter goes after him, finds out its the guy who killed Uncle Ben, and learns with great power with great responsibility like the comics.
Peter gets home from Ben's funeral with his aunt, having the day off school due to the funeral. He goes up to his room and thinks about what he learned earlier, going back to his costume and back to the drawing board with a design. He adds the mask as he realizes that he can't let people get a personal attack on him if he is fighting crime. He does not want anybody at school finding out, Mj and Harry included. He also designs the web shooters so that he has a way of getting around, using that idea to get around after researching spiders and their webbing online.Peter goes to school another day acting more like his usual self, harry and MJ trying to talk to him.They ask him whats been going on with him lately, Peter ignores them trying to keep them a distance for now till he can find out more about what he will do with his powers. We see the Oscorp scientists from before have the first Spider Slayer built, a small but fast machine with tentacles similar to tentacles made by Doctor Octopus. They send it out to find Peter.
Peter goes out for the first day in his Spider-Man costume, testing out his web shooters when he hears a bank alarm. He sees Shocker coming out of the bank, Peter thinks this would be a perfect time to test out his powers in combat. He swings down, making a quip to Shocker and they have a fight. This is also the first time that Peter notices his spider sense, dodging the first blast by Shocker, They have a quick fight only for Spidey to web off Shocker's gloves and crush them in his hands, webbing up the villain.
He takes a breather for a minute only for his spider sense to go off again, and he barely dodges a Spider Slayer coming right at him. It is being controlled at Oscorp by several scientists including one Spencer Smythe. They go after Spider-Man and another fight ensues. Spidey is barely able to keep up with them as they are almost as fast as he is. However, he notices he is starting to not feel very well again during the fight, causing one of the Slayers to get some of his blood. That Spider Slayer escapes back to Oscorp; due to Peter's weakened state, he is unable to follow it.
The scientists start to study Peter's DNA, and we see their faces filled with curiosity. However, they decide that they need his entire body, so they start building the Mark II Spider Slayer. This one is bigger then the previous model, but is not as fast. Peter is in the science lab of his school, designing the spider tracers. He uses an app he is programmed on his cell phone to track the frequency his spider tracers would emit.
However, his spider sense goes off and a team of Mark II Spider Slayers (accompanied by a handful of Mark Is) break into the school, looking for Peter. When the slayers come crashing are looking at all the students trying to find peter, one of them almost hits MJ but before that can happen Harry runs in and gets her out of the way. Before any of the slayers can find him, he quickly changes into his costume and a fight breaks out all over the school. Peter is eventually able to take down all but one Mark I, tricking it into thinking he is gone and throwing a spider tracer on it so he knows where to go.
Smythe is angry with the rest of the crew, berating them for not capturing Spider-Man. Smythe goes into his office to finalize the design of the Mark III Spider Slayer. Peter goes to his room to try and devise a way to beat the Spider Slayers and shut them down for good. He eventually breaks into Oscorp with a new batch of web fluid designed specifically to combat the robots.
Sneaking around and taking out some of the guards, he eventually makes it to the main lab where Smythe comes out of the back in this big door waiting for him. The Mark III Spider Slayer is even bigger then the Mark II, but is even faster due to being similar to an Iron Man suit (Smythe is piloting it from the inside). Smythe is also aided by several Mark Is and Mark IIs. Peter battles Smythe all across Oscorp, destroying several rooms inside the building.
During the battle, the sickness and pain that Peter felt during his first fight returns. He realizes that this is coming whenever he uses his powers for an extended period of time. As Peter makes it to the weapons testing lab of Oscorp, he is able to trick all of the unmanned Spider Slayers into exploding around Smythe, blinding him and causing him to be injured in the explosion. He is barely able get out of the Mark III. He tries to escape before Spidey grabs him. However, Smythe is able to get out of Spidey's grip, falling to his death in the street.
This event causes Spidey to be viewed as a menace. He is eventually able to escape seeing his name slandered all over the news, especially by J. Jonah Jameson. He goes to school the next day seeing everyone except flash thompson insulting Spider-Man for killing Smythe, Flash of course thinking its all a publicity stunt. Peter meets up with MJ and Harry in the Cafeteria, he notices they are holding hands. Peter asks what this is all about and he is told by Harry and MJ that they have started dating, MJ having seen Harry in a new light after he saved her life. This does make Peter a tad confused and jealous but he decides to shrug it off and ask harry if they can go to oscorp so he can get some picutres for the school paper. He goes with Harry into Oscorp days later to visit his Harry's dad, sneaking off to look into the lab. Logging onto the computer with Harry's information, he deletes all of the data on the Spider Slayers. Peter decides to look into the data Oscorp has on Spider-Man. When he gets in he discovers that his DNA is mutating further than before, and that the more he uses his powers, the quicker he that spider part of his DNA will grow.