Following the dissolution of his company, Peter lands on some hard times as Spider-Man due to Kingpin winning the Mayorship for his protecting New Yorkers during Hydra's usurpation, Fisk has been pretending to be Spidey's biggest supporter and managed to put the web-head at odds against the whole superhero community.
Trying to see a positive in his personal life, Peter Parker enjoys his job as a science editor at the Daily Bugle until he is accused by Cindy Lawton of plagiarizing his doctoral thesis from that of Otto Octavius (who occupied his body at that time.)
As this was proven by an advanced computer comparison algorithm… the exposure results in Peter losing his job. He later fights with Aunt May over his hiding from the fallout of his company and the loss of his doctorate.
Trying to think of what to do next, he ventures as Spider-Man he manages to thwart an alien invasion upon discovering that it was all a trick of Mysterio. Realizing a monotony of the encounter, Spider-Man webs Mysterio to a building for authorities to take into custody.
As Peter, he apologizes for everything from his body swap with Otto to his recent attack by Red Goblin, and makes amends with Mary Jane Watson. Reconciled, the two begin dating again and find some measure of glee.