- Spider-Man / Peter Parker
- Sally Avril
- Baxter Institute
- Mister Fantastic / Reed Richards
- Invisible Woman / Susan Storm
- Mary Jane Watson
- Michelle Cage Jones
- Ned Leeds
- Randy Robertson
- Carlie Cooper
- Nathan “Nate” Quil
- Zoe “Zoey” Gillan
- Sam Wilson
- Aunt May
- Edith (first appearance)
- Norman Osborn (mind transferred to Living Brain's body) (flashback and main story) (dies)
- Trapster / Clayton Cole (first appearance)
- Scorpion / Mac Gargan (first appearance)
- Living Brain / The Goblin / “Norman Osborn” (first appearance) (flashback and main story) (mind transferred to Norman Osborn's body)
- J. Jonah Jameson (single appearance) (mind transferred to and from Flash Thompson's body)
- A.I.M. (first appearance)
- Unnamed Agents
- Bilderberg Academy
- Fantastic Four
- Human Torch / Johnny Storm (mentioned only)
- The Thing / Ben Grimm (mentioned only)
- Stan Lee (cameo)
- Midtown High School
- Principal Warren
- Harry Osborn
- Flash Thompson (mind transferred to and from J. Jonah Jameson's body) (removed from team)
- Ashley Kafka
- Otto Octavius (flashback only)
Two years ago, Oscorp was attacked by a deformed Dark Elf referred to as the Goblin, who was teleported to Earth by a malfunction on a Space Stone-powered machine, until he was stopped by Otto Octavius, who vaporized the Goblin's body using the Living Brain. However, the Living Brain is revealed to have become the host of the Goblin's consciousness, and Octavius (who had learned of this) had forcibly shut the Living Brain down and seal it away in one of Oscorp's warehouses. In Present day, two A.I.M. agents arrive to steal tech stored on one of Oscorp's warehouses, until they accidentally reactivate the Living Brain, which is now under Goblin's control. The Goblin absorbs the agents' life forces and sets out to get revenge on the Oscorp employees.
One month after dropping out of Midtown High School, Peter Parker is with his friends enjoying their new enrollment at Baxter Institute as Reed Richards welcomes more new students to the school. In one of their many class lessons, Peter and his friends learn from their top teacher and Richards' wife Susan Storm more about Artificial Intelligence life, and what they require to create their own. Later on, while interning at Roxxon to oversee the A.I. systems stored in there (including prototype A.I. Edith, who takes a liking to him), Peter is met with Midtown High's school reporter Annabelle "Anna" Brady, who interviews him over the students' experiences and progress in Baxter Institute. The interview, however, is interrupted when Flash Thompson comes by to mock Peter again and when Daily Bugle editor J. Jonah Jameson comes by greedily demanding Peter's answers about Spider-Man's identity following his help in defeating the Master Planner, issuing in a argument between Thompson and Jameson which causes Peter to dismiss everyone and call off the interview, and Richards to declare Baxter Institute closed for all who are associated to Midtown High and Daily Bugle; students/interns and staff alike. After a angered Anna accuses the two for ruining her interview and decides to drop out of Midtown High to join Bilderberg Academy, Thompson is scolded at by Principal Raymond Warren and forbidden from participating the football championship as punishment while Jameson is given a restraining order to keep him away from Peter and any student enrolled at Baxter Institute. While still analyzing Edith with Mary Jane Watson, Peter watches Thompson and Jameson bickering and blaming each other for their conditions before he suits up as Spider-Man when the Living Brain emerges to wreak havoc. Spider-Man manages to stop the robot, although one of the Living Brain's turrets accidentally fires two beams at Thompson and Jameson.
As the Living Brain retreats, Spider-Man checks on Thompson and Jameson, who are luckily unharmed, although they continue bickering with each other when Jameson ungratefully berates at Spider-Man for the situation before Jameson forcibly retreats to Daily Bugle when the LMD disguised as Peter arrives. As Spider-Man rushes to the situation and the LMD resumes to oversee Edith alongside Richards and Mary Jane infiltrates the Bugle for evidence of Jameson's involvement with the Living Brain's existence, Thompson attends to a gym class while Jameson continues his work until both feel the growing effects of the Living Brain's laser beam, which simultaneously swaps their minds and bodies. Later on, Spider-Man overhears Richards alerting him that Scorpion and Trapster are after Edith and rushes there to stop them. After defeating the two villains, Spider-Man and Mr. Fantastic find a communication device revealing that someone hired them to take Edith in, and through the records, they believe it is Norman Osborn (who seeks to sabotage Baxter Institute and get Peter to re-enroll at Midtown High) and rush into Oscorp to confront him. Scorpion and Trapster recover and ambush the duo so they can get their reward for Edith. Just then, they discover that it was not Osborn who hired them, but rather the Goblin through the Living Brain, who is eager to get his revenge on Osborn and Octavius.
Meanwhile, Thompson and Jameson begin damaging each other's reputation in Midtown High and Daily Bugle respectively while in each other's body. Thompson trashes Jameson's workplace while beating up and insulting the employees (or "puny nerds" as he calls them) present and threatening to throw them off the building unless they rant about Peter and his classmates until Mary Jane (who was also recording his actions) knocks him unconscious. And Jameson gets into a fight with the jocks who are dressed as Spider-Man and insults the teachers and students (including Ashley Kafka, whom he even forces to write about the "true colors of Spider-Man") before Sally Avril knocks him out. Back in the Oscorp building, Spider-Man and Mr. Fantastic are struggling on their own against the Living Brain, who subdues the pair and prepares to kill Osborn, who has a disturbing vision of the Goblin in it. But before it can finish, Edith (taking control of the robotic owl she was stored in) attacks him, disabling his Neuro-beam guns and allowing Spider-Man and Mr. Fantastic to finish the robot off, reversing the body swap on Jameson and Thompson in the progress. As Scorpion and Trapster are taken back to prison, Peter and Richards see Thompson and Jameson having been sentenced to do community service and clean up garbage after Thompson was expelled from Midtown High and Jameson was fired from the Bugle and arrested for the incidents they both caused as a result of their mind swap; Peter is secretly aware of the swap, but chooses not to discuss about it. Back in Baxter Institute, Peter is entrusted by Roxxon's executives to look after Edith under her wishes to be with him, as he and Richards are unsure if they had seen the last of the Goblin. Later at night, Osborn is shown at his office relieved that "the nightmare is over", but unknown to him, the Goblin's essence (having survived being erased in the Living Brain's destroyed body) has secretly possessed some small bits of Osborn's brain as he mutters: "I'm out... Or should I say... IN?" and laughs diabolically.
- Haley Joel Osment as Spider-Man / Peter Parker
- Ashley Johnson as Mary Jane Watson
- Lacey Chabert as Sally Avril
- Alan Tudyk as Mister Fantastic / Reed Richards
- Catherine Taber as Invisible Woman / Susan Storm
- Scott Menville as Nathan Quill
- Laura Bailey as Zoe Gillan
- Bumper Robinson as Sam Wilson
- Alanna Ubach as Michelle Cage Jones
- Zeno Robinson as Randy Robertson
- Tara Strong as Carlie Cooper, Edith
- Eric Bauza as Ned Leeds
- Jennifer Hale as Aunt May
- Hynden Walch as Annabelle Brady, additional voices
- Terrence C. Carson as Nick Fury
- Sam Riegel as Harry Osborn
- John DiMaggio as Principal Warren, J. Jonah Jameson
- Jeffrey Combs as Norman Osborn, Living Brain / The Goblin
- Will Friedle as Flash Thompson, Trapster / Clayton Cole
- Liam O'Brien as Scorpion / Mac Gargan
- C. Thomas Howell as Otto Octavius
- Marisha Ray as Ashley Kafka
- The moment Flash Thompson and J. Jonah Jameson interrupt Annabelle Brady's interview with Peter Parker had a similar effect to Eddie Brock ranting on Carlton Drake over his allegations in the 2018 film Venom. Like Brock was fired from his job as journalist, Thompson was suspended from the school football team while Jameson was given a restraining order.
- Additionally, Sally Avril, responding to Thompson's failure, says: "You did this, Flash. Not Anna, not Peter Parker, not Reed Richards. You." similarly to Anne Weying during Brock's failed reunion with her.
- The ending of this episode is similar to the Transformers: Prime episode "Sick Mind", on which Megatron had also managed to transfer his consciousness from his inactive body to Bumblebee's mind after Bumblebee entered Megatron's dream.
- The Goblin's lines: "I'm out. Or should I say... IN?" are also the same of Megatron in the show.