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Spider-Man (real name Miguel O'Hara) is a prodigal geneticist of Irish-Mexican descent. He resides in an alternate universe that takes place in the year 2099. He is voiced by Freddy Rodriguez.
In part one of The Spider-Verse, the Green Goblin uses a device known as the Siege Perilous, using Electro as a living power source, to travel to a futuristic dimension that takes place in the year 2099 to find the Spider-Man of that universe, in order to steal his DNA. However, the Spider-Man of his universe, the "Ultimate" Spider-Man, arrives in the dimension as well. Spider-Man is amazed at the advanced, futuristic New York City, before noticing a robbery at Alchemax by robotic drones. Spider-Man battles and defeats all but one drone. However, a Spider-Man dressed in a blue metallic costume comes in and trashes the robot right as it's about to attack Spider-Man. Spider-Man is amazed at Spider-Man 2099's costume, only for the latter to attack him. Miguel questions Peter if he is an android or a clone, which Spider-Man declines, stating he is a counterpart. Spider-Man 2099 is unconvinced and continues attacking Spider-Man. Peter continues to try and convince Miguel that he is a counterpart. Miguel finally relents, telling Peter that he "doesn't know who you're pretending to be". He tells Peter that "Spider-Man is just a legend that someone is trying to recreate....unsuccessfully". However, they are attacked by the Green Goblin. Spider-Man and Spider-Man 2099 battle the Goblin, though they fail to stop him from stealing a blood sample from Miguel. Having gotten what he sought in the future, Goblin blasts missiles at the building's top level to distract the Spider-Men before opening another time portal to escape. Spider-Man and Spider-Man 2099 stop it by interweaving their webs together in order to make a cable strong enough to keep the building from collapsing. Miguel thanks Peter for helping him, and Peter tells him that New York will always need a Spider-Man to protect it, and the two bid each other farewell.
Spider-Man 2099 later reappears in part four, summoned by the "Ultimate" Spider-Man, alongside several other alternate Spider-Men, Spider-Man Noir, Spyder-Knight, Spider-Girl, Spider-Ham and Ultimate Spider-Man to form the Web-Warriors in order to combat Spider-Goblin, an arachnid-esque form of the Goblin caused by injecting himself with a serum composed of every Spider-Man's DNA. The Web-Warriors battle Spider-Goblin, and with the help of Electro, manage to depower him, turning him back into Norman Osborn. However, Electro then betrays them, merging himself with the Helicarrier, transforming it into a massive battle mecha. The Web-Warriors distract Electro while Spider-Girl and Spider-Ham manage to shut down the Helicarrier. After Spider-Man defeats Electro, Spider-Man 2099 returns to his dimension, along with the rest of the Web-Warriors.
- In the original comic series, Spider-Man 2099's universe is the same universe as original Spider-Man's original universe, but in a distant future. As explained in Edge of Time game and Superior Spider-Man comic series, prior both universes are revealed to be one and the same in a different timeline.
- Unlike the original comics, this animated Spider-Man 2099 has a spider-sense ability.