Miguel O'Hara is born in New York City, many years after the end of what his people's history calls the "Heroic Age", which is the modern day era of Marvel heroes. He grows up with his mother Conchata, his younger brother Gabriel, and the abusive father George O'Hara. A rebellious boy with prodigy-level intelligence, Miguel is an adolescent when he is awarded enrollment into the Alchemax School for Gifted Youngsters (heavily implied to be a renovated version of the X-Men's headquarters) in Westchester, owned by the powerful Alchemax megacorporation which also controls local law enforcement agencies. Here, he befriends Xina Kwan, a girl of similar intelligence who specializes in computers. Xina helps Miguel defend himself against the bully Kron Stone, son of Tyler Stone: Vice President of R&D for Alchemax.
As adults, Miguel and Xina date seriously until Miguel cheats on her with Dana D'Angelo, who originally is the girlfriend of Miguel's brother Gabe. Later on, Miguel and Dana are engaged. Though seemingly arrogant and confident in all walks of life, Miguel is a very private man and trusts almost no one save for his apartment's holographic aid Lyla, an artificial intelligence programmed by Xina.
Origin as Spider-Man
Miguel eventually becomes head of the genetics program of Alchemax, intended to create new corporation-controlled super-powered soldiers called "corporate raiders." Miguel is specifically inspired by surviving records concerning Spider-Man and hopes to one day create a similarly powered person. But after a human test subject dies during an early experiment, Miguel tells Tyler Stone he wishes to resign from Alchemax and discontinue his genetics research. Rather than let Miguel leave, Tyler Stone tricks him into taking Rapture, an addictive drug that genetically bonds to the user. Tyler reminds Miguel that only Alchemax is allowed to legally distribute this drug, so if O'Hara does not remain with the corporation then Tyler must assume he is getting the drug from the black market and will be forced to tell the police. Not wishing to be a blackmailed addict, Miguel recalls that he entered his own genetic code into his machine's databanks during initial experiments, using it as a human DNA test sample. Intending to use this older template of his pure genetic code to write over his current biology and free himself from the Rapture, Miguel sneaks into Alchemax and uses the gene alteration machines on himself.
After Miguel turns on the machine to rewrite his DNA, his jealous subordinate Aaron Delgado sabotages the machines, causing them to alter Miguel's genetic code to be "50% spider DNA." Miguel survives the process, but realizes he now has spider-abilities.
Realizing that there is now a person with abilities similar to Spider-Man, Tyler Stone sends agents to hunt this person. To conceal his identity while he fights his pursuers, Miguel dons a bodysuit with a mask that he once wore for the Mexican Day of the Dead festival. Miguel chooses this costume in particular because it is the only clothing he has that is made from "UMF" (Unstable Molecule Fabric), meaning it is the only clothing he owns that will not be torn or shred by the spider-talons that now occupy his hands and feet. After seeing him operate in public, a group of Thorites (worshipers of the Marvel hero Thor) come to believe that Miguel is the legendary Spider-Man back from the dead, and that he is the harbinger of Thor's eventual return.
Originally focused with finding a cure for his condition, Miguel's further adventures as Spider-Man 2099 cause him to realize how ignorant of the world he was and how he had turned a blind eye to the oppression and pain the corporations of the world have caused. He is also surprised at the effect his presence has on the people who have been oppressed for so long, particularly his own mother, who ironically also hates the man her eldest son has become, admires the exploits of Spider-Man 2099. After this, Miguel decides to embrace his identity as Spider-Man. Donning his costume, he publicly proclaims himself to be an enemy to all the megacorps, saying he will use his powers to fight for ordinary people against those in power who abuse their influence and authority.
Later on, Miguel discovers that an arrogant scientist at Alchemax called Jordan Boone is conducting "Virtual Unreality" experiments to create a doorway into another dimension. These experiments lead to the release of two mysterious figures: the Net Prophet, called "the prophet of Thor" by the Thorites, and a powerful megalomaniac called Thanatos. The Net Prophet becomes a new ally to Miguel. Since the Net Prophet is believed to be Thor's prophet, his association with Spider-Man 2099 leads more people to believe that Miguel's alter ego is the harbinger of Thor.
In the "Time Flies Saga" that occurs years later in Peter David's Captain Marvel series, it is revealed that the Net Prophet is actually the hero Justice (John Roger Tensen) and that Thanatos is a corrupt version of Rick Jonesfrom Earth-9309.
The first major crossover of Marvel 2099 happens when Miguel and Dana visit Alchemax's floating city "Valhalla" and are startled by the sudden appearance of two men claiming to be Thor and Heimdall, respectively. It is later discovered that Alchemax CEO Avatarr has transformed ordinary people into duplicates of the Asgardians in order to eliminate the rising influence of new superheroes over the public. By joining forces, Doom, Ravage, thePunisher (Jake Gallows), the X-Men, and Spider-Man 2099 are able to defeat the fake Aesir, and Valhalla falls.
Miguel later learns that Gabe is aware of his dual identity, having recognized Spider-Man's costume from what Miguel wore to the Day of the Dead festival years earlier. Gabe has grown a bit resentful of Miguel's new heroic career, particularly since his girlfriend Kasey seems enamored with the costumed Spider-Man 2099.
After his holographic aid Lyla suffers a serious malfunction, Miguel asks for repairs from his ex-girlfriend Xina. Dana later accuses Miguel of cheating on her with Xina. Miguel becomes angry about this and about Dana's noticeably increasing interest in Tyler Stone. The two dissolve their romantic relationship, and Xina and Miguel become companions again.
Spider-Man 2099 Meets Spider-Man
In the 1995 one-shot Spider-Man 2099 Meets Spider-Man, Miguel and Peter Parker, the Spider-Man of the Heroic Age, find themselves having switched places, with Miguel waking up next to Peter's wife, Mary Jane, and Spider-Man finding himself in the future. They discover that their predicament is caused by Fujikawa (in the Modern Age) and Alchemax (in the year 2099) running experiments on a temporal energy generator. While Peter tackles the Vulture of 2099, Miguel faces Venom (Eddie Brock). Miguel realizes that this temporal anomaly is what will cause the end of the Heroic Age, since where he is in the past is when history tells him all the heroes and much of Earth's culture and technology were wiped out.
The two Spider-Man characters were united to face a major cause of the chaos, a time-traveling female Hobgoblin of the year 2211 (Robin Borne) from the alternative universe of Earth-9500. They are aided by this Hobgoblin's father, Spider-Man (Max Borne), and eventually everyone is sent back to their respective times.
It is noted at the end of this adventure that by being in the past, Miguel has slightly altered his present world of 2099 since his actions have postponed the end of the Heroic Age to a now-unknown date. This implied that the world of Marvel 2099 might no longer have been the definite future of the modern Marvel Universe and in later stories it was said that Marvel 2099 occurs on the parallel world of Earth-928 (mainstream Marvel stories occur on Earth-616).
Revelations, Nightshade, and "One Nation Under Doom"
While eavesdropping on a conversation between his mother and Tyler Stone, Miguel learns that the Rapture that Stone gave him was only a short-lasting simulation and would have worn off in time. He also learns that Tyler Stone is his real father. Bothered by this, he leaves New York to go traveling with Xina. During this time, they travel to Nightshade, an independent research town (free of megacorp rule) run by Angela Daskelakis, their former headmistress at the Alchemax institute. While they are visiting Alchemax attempts a hostile takeover of Nightshade, destroying most of the city and killing Angela in the process. Xina returns home and Miguel disappears into the desert, saved by a group of scavengers. As Spider-Man, they ask him to try and fix an old homunculus-like robot they had found. After seeing Spider-Man's mask, it transforms itself into a hybrid of the present day Spider-Man and Venom, naming itself Flipside. Seemingly harmless at first, the robot begins showing psychopathic and homicidal tendencies. Miguel escapes, leaving the scavengers to Flipside's mercy and returns to New York.
Upon his return, Miguel finds out that Doom 2099 has assumed control over the U.S. and its megacorps. Tyler Stone is appointed as Doom’s Corporate Minister and Miguel is offered the seat of CEO of Alchemax. Later, Doom 2099 offers Spider-Man 2099 the position of Minister of Supernormal Affairs. Miguel eventually accepts the position at Alchemax, deciding to change the company for the better. He also uses his new influence to order law enforcement to leave Spider-Man 2099 alone.