- Main article: Spider-Man (film)
Mary Jane is Peter Parker (Tobey Maguire)'s childhood and high school crush and only sweetheart. At the time, she is dating the high school bully, Flash Thompson (Joe Manganiello), but breaks up with him at their high school graduation ceremony. Desperate to escape her abusive, alcoholic father, Mary Jane begins to pursue a career in acting, but she secretly waitresses at a diner after being rejected at an audition. Peter's friend, Harry Osborn (James Franco), is her first boyfriend after leaving high school, but she becomes attracted to Peter's alter-ego, Spider-Man, after the superhero saves her from the Green Goblin. She later shares a passionate kiss with Spider-Man while he is suspended upside down after he saves her from a gang of thugs. Shortly after Harry proposes Mary Jane begins to grow more distant from Harry, denying his advances. Her feelings for Peter grow when he tells her what he supposedly told Spider-Man about her. After Harry sees Peter and Mary Jane holding hands, he gets angry and breaks up with her.
Harry's father Norman Osborn (Willem Dafoe) knows of Spider-Man's secret identity and finds out about his feelings for Mary Jane from his son. As his criminal alter-ego, the Green Goblin he kidnaps her and holds her over the Queensboro Bridge, telling Spider-Man that he must choose between her and a group of children caught in the Roosevelt Island tram car. Spider-Man saves both Mary Jane and the children, however. At the end of the film, Mary Jane tells Peter that she loves him and they kiss. However, Peter shies away from her as he is afraid for her safety, and thus does not want to get involved with her. She is heartbroken by his rejection, but realizes that her kiss with Peter reminded her of the one she shared with Spider-Man and suspects that he is the superhero.
- Main article: Spider-Man 2
Mary Jane wants to start a relationship with Peter, who still resists because he fears for her safety. In her frustration Mary Jane goes on to have a relationship with John Jameson (Daniel Gillies), the astronaut son of Daily Bugle publisher J. Jonah Jameson (J.K. Simmons). Prior to this, Harry said that she was waiting for him. Much to Peter's delight, he sees her billboard picturing her modeling for a perfume near the pizza place he works at.
Later, Peter decides that being Spider-Man is not what he wants and he attempts to start a relationship with her. Mary Jane pushes him away this time because she is getting married to John Jameson, but secretly does want a relationship with Peter, although she tries to convince herself otherwise. She is also angry at Peter because he fails to see her star in The Importance of Being Earnest, which John, Harry, and Aunt May have seen, some of them more than once. (Even her father went backstage to ask for money.) When Peter does arrive to see it the first time, a snooty usher (Bruce Campbell) stops him for being late. The second attempt to see it, which is successful, is when he tries to reconnect with her. After Mary Jane kisses John, in a manner that is reminiscent of the upside-down kiss between she and Spider-Man from the first film, she finds that she may want a relationship with Peter.
She meets Peter in a coffee shop where she asks for a kiss to confirm her belief that he is Spider-Man. She even asks him if he loves her, to which he falsely replies,"I don't", for the sake of his superhero responsibilities and her safety. Just before Peter can kiss her, Doctor Octopus (Alfred Molina) kidnaps her and runs away. Doctor Octopus takes her to an abandoned pier where Spider-Man confronts him. Spider-Man pulls his mask off in hopes of getting Doctor Octopus to come back to his senses, and Mary Jane sees that Spider-Man and Peter Parker are one and the same. After Doctor Octopus reforms and sacrifices himself to save New York, Spider-Man and Mary Jane share a moment together, where Spider-Man finally admits that he does love Mary Jane, but cares more for her safety.
At the film's end, Mary Jane prepares to marry John Jameson, but she leaves him at the altar, goes to Peter's apartment, and reveals that she loves Peter and is prepared to face whatever risks their relationship may bring.
- Main article: Spider-Man 3
Both Mary Jane and Harry now know that Peter is Spider-Man. In the film, Peter is intending to ask Mary Jane to marry him. When he reports the good news to his Aunt May (Rosemary Harris), she is delighted and asks Peter to give her engagement ring as a gift to Mary Jane. However, Peter becomes slightly overconfident due to Spider-Man's success. Meanwhile, Mary Jane's Broadway debut takes a turn for the worse when her performance gets bad reviews. Unaware of this incident, Peter accidentally pushes Mary Jane away, thinking he understands her situation. She also begins a rivalry with Gwen Stacy (Bryce Dallas Howard) for Peter's affections. Having been replaced on Broadway by her understudy and then having to work at a jazz club, Mary Jane and Peter's relationship worsens when Spider-Man is unexpectedly kissed by Gwen Stacy in front of a whole crowd of people the same way Mary Jane kissed Spider-Man in the first film. When Peter attempts to propose to Mary Jane that same night, Gwen appears at the same restaurant and talks with him; Mary Jane leaves, furious.
Mary Jane, feeling alone and despondent, calls Harry, who recently lost his memory and hatred of Spider-Man after being defeated in an aerial battle as the New Goblin. They renew their bond, and in a moment of joy, Mary Jane kisses Harry. Realizing what she is doing, Mary Jane quickly leaves; the emotional turmoil restores Harry's memories and his mission to destroy Spider-Man as the New Goblin. He confronts MJ in her apartment, and threatens to kill Peter if she does not break up with him. Following Harry's orders, she breaks up with Peter. Peter, heartbroken and upset, refuses to tolerate these tragedies, and turns to the symbiote suit, which enhances his aggression.
One night, Peter decides to go to Mary Jane's jazz club with Gwen. He shows her up on stage by playing the piano, and makes a big show of dancing with Gwen. Gwen, realizing that she is being used as a prop to make Mary Jane jealous, apologizes and leaves. Mary Jane is still visibly shaken when Peter confronts her at the bar, and he is assaulted by two of the club's bouncers. A fight ensues, and Mary Jane tries to stop Peter. Thinking she is another bouncer, Peter strikes her. Peter, realizing what the evil symbiote is trying to do, leaves the club.
Peter tears the symbiote off his body at a church bell-tower. During the struggle, it falls on Eddie Brock, Jr. (Topher Grace) standing below and creates Venom. At his apartment, Peter fears that even though the symbiote was responsible for current events, he may not be able to put Mary Jane first, and gives his wedding ring back to Aunt May, who convinces him that if he tries his best, he can put things right. Peter then goes to Harry in desperation, because he needs help against his new foe. Harry turns him down, but changes his mind after his butler reveals that Norman Osborn had in fact killed himself. Meanwhile, Venom kidnaps Mary Jane, holding her hostage at a construction site, where a climatic battle takes place between the team of Venom and the Sandman (Thomas Haden Church) against Spider-Man and Harry Osborn, a.k.a. the New Goblin. During the fight, Harry defeats Sandman, but is impaled by Venom with his own glider after jumping in the way of Venom attempting to impale Peter. After Peter defeats Venom, he goes over to the mortally wounded Harry, alongside whom Mary Jane is also present. Harry dies in Mary Jane's arms after mending his friendship with Peter.
After attending their friend's funeral, Peter and Mary Jane reconcile.