The Story starts with Dr. Wirtham preparing the Neurolitic Scanner he stole previously in order to scan his patient, Amy Chen's brain and detect her damaged area, however it becomes difficult due to the complexity of the device and Cardiac replies that the only one who can handle it properly is Otto Octavius.

Meanwhile, Otto fights against the Avengers, avoiding them thanks to his Spider-Sense, but Peter's voice during the conflict distracts him long enough to be knocked down by Spider-Woman's Venom Blast and Captain America's shield, preparing him for his tests. Also, Carlie Cooper has become completely sure that Spider-Man is not Peter, but she can't rely this information to the Avengers or the media until she gets solid proof, so she contacts someone who agrees to help her.

The Avengers perform many tests on Otto's body, and after a few minutes, the results appear positive, revealing that Otto is not a Skrull or is being manipulated by outside sources confirming that he is indeed Spider-man, much to Peter's dismay. However, Otto discovers a minor brain anomaly that would've revealed his condition but no one else seems to notice it, so he takes notes of the results by himself.

The Avengers apologize, but Captain America warns Otto that he's on probation and if he keeps on with another brutal assault he will be expelled from the team. Natasha talks to Otto, arguing that she seems to understand his changes after what they had been through when Otto almost burned down the planet (during the events of Ends of the Earth) and that seems to have changed Peter.

While she tells him that he now carries "Red on his Ledger", she lets him know that if he wants to discuss about crossing the line, she'll be there for him. Peter tries to warn Natasha to no avail, until, taking advantage of Otto's distraction, manages to draw a picture into the notepad. Natasha notices it after Otto leaves, but she discards it as just a lame drawing.

Otto returns to patrol, relieved that the Avengers failed to notice that brain anomaly and thankful that Tony Stark and Hank Pym, the only ones who would've noticed it, were absent. Otto returns to Horizon Labs and check the details of the anomaly, realizing that to complete his research he must retrieve the Neurolitic Scanner.

While Cardiac prepares for the surgery, the alarms of the H.E.A.R.T. Clinic go off, and once he's preparing as Cardiac, he discovers the Spider-Tracer, only to be intercepted by Spider-Man. Otto demands that he surrenders the device but Cardiac refuses starting a fight in the hospital.

While Otto tries to fend off the attacks, Cardiac tries to delay him but fails. Otto finds the Neurolitic Scanner on Amy's head and even tries to retrieve it but Peter refuses to allow him to do so until Cardiac manages to stop him. Otto demands an explanation and Cardiac reveals that when Otto tried to kill the planet with his Heat Satellites, he didn't considered about those who were already sick like Amy, whose parents died in an accident caused by his scheme and she barely survived with severe brain damage. Otto feels remorse for the consequences and decides to assist Cardiac and his medical crew with the surgery, arguing that he spent years studying Doctor Octopus' technology and even offers to perform it himself.

Even though Otto is having minor afflictions with his hand, the surgery is a success. Cardiac thanks Spider-Man for the help and Otto replies that he was wrong about him and offers his help on anything, which makes Cardiac allow Otto to take burrowed his Neurolitic Scanner.

Back at Horizon Labs, Otto rejoices in his win but Peter warns him that he will still fight to recover his body, only to be shocked by discovering that Otto has found him, being the brain anomaly the Avengers detected and asks his robot assistant, The Living Brain, to prepare the lab for a "Parker-Ectomy"