The first volume, that ran between January 2013 and September 2014, was written by Dan Slott, with artwork by Ryan Stegman, Humberto Ramos, and Giuseppe Camuncoli, continuing from the events of the 2012 storyline "Dying Wish", in which Peter Parker is killed off and replaced with his nemesis Otto Octavius, who swapped consciousnesses with Parker and left him to die in his decaying body to ensure his own survival.

The same year, a second volume of The Superior Spider-Man debuted as part of the "Spider-Geddon" with 12 new issues, written by Christos Gage and drawn by Mike Hawthorne.

[7] In December 2018, Otto, in his Superior Spider-Man avatar, returned once again in a series written by Christos Gage and illustrated by Mike Hawthorne.

[8] In June 2023, it was announced that a new volume of The Superior Spider-Man would launch later in 2023, which also the 10-year anniversary of the original storyline, and that Dan Slott would return to write the book.

[10] When his old Sinister Six teammate Vulture resurfaces, Octavius attempts to convince Parker's old friend Harry Osborn to give up crime.

[13] His decision to execute Massacre sits ill with his teammates in the Avengers and they bring him in for questioning after a brutal beating of pranksters Jester and Screwball.

[33] The Goblin King destroys everything Otto created/saved to build his new legacy: his childhood home, the research center where he created his arms, the "BoneYard" where all his paraphernalia is held, the soda factory where he did his first heroic act, and the HEART Clinic.

[36] During the time Superior Spider-Man was missing after the Horizon Lab explosion,[24] he was teleported to 2099, where he used the future technology to find a way back, but instead discovers the existence of the Inheritors.

After finding out his original body has been stolen by New U Technologies and was being restored, Otto infiltrated New U's lab and transferred his consciousness into his renewed body and quickly destroyed a copy of Peter Parker's consciousness, created as a side effect of Peter inhabiting Otto's body as it died, before reclaiming his title as Dr. Octopus and making a pact with The Jackal (who was secretly Ben Reilly, a clone of Peter Parker having initially been a hero, but due to being killed and resurrected countless times by Miles Warren, his creator and the original Jackal, he was driven over the edge and for the time being went down a more malicious path) to perfect New U Technologies' currently flawed cloning process.

Otto later defects from Hydra, deciding to resume his former self's career in heroism and bases himself in San Francisco, using the alias of "Eliot Tolliver", and gains a position at Horizon University.

[40] Superior Octopus establishes himself as the local hero of San Francisco, where he has defeated the Night Shift, Arnim Zola, and Count Nefaria.

[41] Spider-UK, Spider-Woman of Earth-982, Spider-Gwen of Earth-65, Doctor Octopus (Octavia Octo) of Earth-1104, Spider-Ham, Spider-Punk of Earth-138, and Spider-Man Noir gather at the lab to warn him of the risk.

His identity as Dr. Elliot Toliver is uncovered by Anna Maria, who confronts him with the rebuilt Living Brain, but the appearance of Terrax gives Otto a chance to temporarily evade this.

Despite lacking the weaponry, technology, and the Night Shift's assistance (who ran away in fear after one of their undead members is cut in half) to take on Terrax, Otto refuses to back down despite being heavily injured during the fight against him.

At the fight's conclusion, Superior Spider-Man asks if Doctor Strange could cast the same spell that he used to make the world forget about Peter's identity.

Doctor Strange rejects that request as the original spell could only be cast under specific circumstances and in any case he feels that it does Superior Spider-Man good to have people aware of his past so that he won't be tempted to "regress".

In Horizon University's sub-basement two, Superior Spider-Man states that they will not be able to power the dimensional transporter without something that can replicate the energies of the Cosmic Cube.

As Max Modell and Emma Hernandez are loaded onto the ambulances, Anna Maria Marconi tells Superior Spider-Man that she will go to the hospital to keep an eye on them.

Spider-Man of Earth-44145 states that he will spare of James if he kills three citizens in front of the cameras that does not involve cheating, criminals, or terminally-ill patients.

Awakening in the infirmary, Superior Spider-Man learns from Anna Maria that James' aunt and uncle are in shock, Skein and Dansen are recovering form their injuries, and Emma is in a medically induced coma while Digger is still living with his head detached while asking for a staple gun.

As Doctor Octopus watches from afar, Digger is informed to distribute the severance pay to the remaining members of the Night Shift so they will not bother him again and to warn them not to go visit the Brothers Grimm in the hospital.

[51] It was revealed at the 2023 San Diego Comic-Con that a one-shot issue entitled Superior Spider-Man Returns would be released in October 2023 for the character's 10th anniversary.

[52] As Otto Octavius arrives at the sight of his infamous accident that turned him into Doctor Octopus in the first place, he works to get to the sub-levels and find what he needs to finally rid himself of his greatest enemy.

Back at Horizon Labs, Otto begins works on making a miniature star with Living Brain present as they are visited by Grady Scraps.

When she arrives at the abandoned Atomic Research Center, she meets up with Spider-Man and the Living Brain where they spend days working together to create a sustainable miniature sun.

Upon entering his lab, he finds Estrella transformed into an energy being after she merged with the miniature sun, as she begins attacks him over the problem that she solved while taking on the name of Supernova.

[55] Initially when it was announced that Marvel was killing off Peter Parker and that his body would be taken over by Doctor Octopus it was criticized universally by fans of the previous series.

While inside the web-slinger's body, Octavius efficiently balances out crime-fighting with his regular life and befriends Midtown High assistant science teacher Anna Maria Marconi.

After Venom attacks and takes Marconi hostage in exchange for the "real" Spider-Man, Octavius realizes the error of his ways just as Peter arrives and reverses the consciousness transfer.

In the episode "The Deception Verification", Howard Wolowitz complains about this comic while Raj Koothrappali says the storyline combines elements of Spider-Man and Freaky Friday.