Michelle Jones was a student at Midtown School of Science & Technology, a member of the Academic Decathlon team, and a classmate of Peter Parker. A loner, she regarded Peter and his friend Ned as losers.

When Academic Decathlon captain Liz Allan hosted a party, Michelle attended. However, when Peter and Ned arrived, she called them losers for attending the party while deeming the party as "lame." Ned pointed out the hypocrisy, but she shrugged the comment off.

Jones joined the team in Washington, D.C. for the academic decathlon finals. She correctly answered the last question of the Decathlon, winning the competition for the team. Mr. Harringtontook them to the Washington Monument to celebrate. Jones refused to go inside with the rest of the team, due to the fact that monument was built by slaves. Fortunately, she was not on board the elevator when an explosion trapped her classmates on it. When Spider-Man arrived on the scene, she pointed him in the direction of her friends.

Jones joined Peter when he was in detention for skipping class. When Coach Wilson asked her why she was there despite not having detention, she claimed that she enjoyed sketching people in crisis.

Jones later attended homecoming, giving Peter the middle finger when he arrived. However, she watched as he fled the scene.

After homecoming and the revelation that Liz's father, Adrian Toomes, was a big time criminal, Liz was forced to move to Oregon, and Jones took her spot as Academic Decathlon captain. Jones told her teammates that her friends call her "MJ". When Peter got a text message and had to leave, Jones inquired his actions, then quipped that she was kidding and did not care

MJ was disintegrated by Thanos alongside half of the universe in 2018, and was resurrected by Bruce Banner five years later. With the resurrected students having disintegrated before finishing the school year, they were forced to restart the school year anew.

Eight months later, MJ attended a school field trip to Europe. Though Parker planned to sit next to her on the flight to Venice, she instead sat next to Brad Davis, a Snap survivor who was the most charming student in the school. In Venice, she developed a fondness for the Italian slang word "Boh," and noticed that Peter had bought something. However, the Water Elemental soon attacked, but was seemingly defeated by a superpowered man Ned and Betty Brant later dubbed "Mysterio."

Though Peter and MJ had a quiet moment looking forward to Paris, the next day saw their trip abruptly diverted to Prague. After a quick stop in Austria, Brad tried to show MJ a picture he had taken, but an odd episode resulted in the photo being deleted. Though the class was supposed to attend a regional festival, that was soon redirected to attending an opera. Peter left the opera house with MJ following close behind.

At the festival, MJ bore witness to Mysterio and a seemingly new hero named "Night Monkey" fighting the Fire Elemental and noticed a camera covered in Spider-Man's webs. The trip was cancelled due to concerned parents, resulting in Peter and MJ having one last night out in Europe. She revealed the camera, causing Peter to confirm her suspicions that he was Spider-Man, and the two realized that Mysterio was a fraud and the real mastermind behind the Elementals. Back at the hotel, Peter decided to go to Germany while ordering Ned and MJ to lie that he was meeting with family.

However, Mysterio once again altered the itinerary to London, where he planned on using a fusion of the Elementals to kill MJ, Ned, and anyone else who knew Spider-Man's identity. There, Brad once again tried to make himself better than Peter, but MJ and the others shut down his story. When the Elemental Fusion arrived, MJ, Ned, Betty, and Flash met Spider-Man's ally Happy Hogan, who led the away from the fusion and Mysterio's drones. Spider-Man eventually defeated Mysterio and revealed his gift: a black dahlia necklace, broken from the attacks. At this, MJ and Peter began a relationship together.

The couple returned to New York, where Peter decided to take MJ out on a date. Shortly after swinging around New York, though, they discovered that Mysterio had sent J. Jonah Jameson of The Daily Bugle doctored footage blaming Spider-Man for the attacks and revealing Peter's secret identity, which Jameson broadcast in front of New York

Following this, the public surrounded MJ and asked her whether she was Spider-Man's girlfriend. Peter swung her out of there, but their troubles were not in the least bit over. MJ was taken to be Peter's assistant in crime and taken to police investigation where she denied all statements against her. Soon after this, Peter, MJ and Ned were denied admission to MIT because of the allegations against Peter. 

Wracked with guilt, Peter visited Doctor Strange to make the world forget Spider-Man's secret identity, but he accidentally botched Strange's spell, which sent several people from other universes into Earth-199999. On Strange's advice, Peter tried to intercept an MIT admissions officer to get her to reconsider their applications, and after saving her from an alternate Doctor Octopus, she gratefully decided to readmit the three back to MIT.

With Doctor Strange having captured an alternate Lizard, Peter enlisted Ned and MJ's help to capture the other alternate supervillains. With their help, Peter was able to capture Electro and Sandman. After Peter captured Norman Osborn, Strange prepared to send the supervillains back to their home realities, but Peter, convinced by his Aunt May to save them, fought Strange and took his corrupted spell from him. Peter gave the spell to MJ, instructing her to use it if his attempt to save the supervillains went awry.

MJ and Ned hid in Ned's grandmother's house, concerned about Peter's lack of a warning. Ned discovered that he had an innate gift for magic, using Strange's sling ring in an attempt to summon Peter. However, he accidentally summoned Peter-2 and Peter-3, the Spider-Men of the villains' realities. MJ and Ned led the other Spider-Men to Midtown High, where they found Peter-1 moping over May's death. Cheered up by his variants, Peter-1 joined his fellow Spider-Men in making cures for the supervillains.

The Spider-Men gathered at the Statue of Liberty to cure the supervillains in a final battle. Ned opened a portal there from the school to hide the spell, but was unable to close it, resulting in the Lizard chasing him and MJ. However, Peter-1 was able to restore the Lizard back to normal. Osborn, corrupted by his Green Goblin persona, joined the fray and used his bombs to free the corrupted spell, breaking part of the statue and causing MJ to fall. Peter-1 tried to save her, only for the Goblin to intercept him. Luckily, Peter-3 saved her instead, redeeming himself for the death of Gwen Stacy years ago. MJ noticed him shedding tears of relief.

Once the villains were all cured, the corrupted spell started fracturing reality, causing many more people who know Peter Parker is Spider-Man to start coming in. Strange, who had been freed by Ned earlier, was forced to create a new spell to send the multiversal people back whence they came at the cost of making everyone forget that Peter Parker is Spider-Man. Peter-1 shared one last exchange with MJ and Ned before the spell was cast, sending the multiversal villains and the other Spider-Men back home.