- Hawkeye (Clint Barton)
- Pepper Potts
- James Rhodes
- Tony Stark (Mentioned)
- S.H.I.E.L.D. (Mentioned)
- Spider-Man (Peter Parker) (Mentioned)
- Justin Hammer (Photo) (Andros Stark reality)
- Hawkeye (Mentioned)
- Justin Hammer (Photo) (Unknown reality)
- Earth-TRN509 (Mentioned)
- Hyperpulse Mark IX (First appearance)
- Iron Man Armor MK II
- Hawkeye's Bow & Trick Arrows
- Black Widow's Gauntlets
Pepper has dragged Tony out shoe shopping, hoping for a day free of computer talk and armory... when a mysterious figure appears in the sky over New York, asking for Iron Man! His scanners find Tony, and chase the two into an alley. He reveals himself to be Tony's time-travelling grandson, Andros Stark. Tony remains skeptical, and he calls for his armor. Andros teleports them out, and informs them that both teleportation and time traveling armor is something Tony will eventually invent... but he will also destroy the world! In Andros' future, Tony has created an artificial intelligence called VORTEX, meant to bring peace - but instead it merges with S.H.I.E.L.D.'s computers, eventually thinking humanity evil and eradicating all life. Tony immediately promises to never invent such a thing, but Andros informs him that he is actually there to execute him. Tony leaps off the building, his armor finally arrives. Andros shrugs off his attacks while Tony points out that killing him now means he'll never be born - a sacrifice Andros is willing to make. He tries to disable him via Extremis, but Andros has his own, much newer Extremis system. His rampaging soon summons the police, giving Iron Man a window to escape while Andros pacifies them.
At Hammer Tower, Sasha is beating Justin at chess. The news come on, displaying Iron Man and Andros' battle, Justin laughs at Andros' armor, calling him Captain Glowstick. Andros then arrives at the office, asking for Justin's help against Iron Man - in 2099 Justin is still alive, and widely regarded as a hero and the smartest man in the world - elected president for third term. Justin is eager to know more about his glorious future, but Andros will not divulge anything, lest they risk changing it. He can only make one more time jump before his armor burns out, so he has to solve his Iron Man problem without it. Hammer hands some worthless Iron Man armor specs, claiming they will allow Andros to track him. At the Armory, the gang swear to never tell anyone - even their future families - about the armory, since it is safe from Andros now it must mean they never did. Tony creates some nanovirus chips based on the Technovore to exploit a weakness in the Extremis biotech... he thinks it can maybe shut down Andros for three seconds. But the chips are very delicate, so he must ask Hawkeye to deploy them.
Unsuccessful in tracking Iron Man, Andros returns to Hammer, who suggests he go after S.H.I.E.L.D. instead, since they are the other half of VORTEX. Justin secretly wants him to fail, as the future where he is president will not happen if VORTEX doesn't happen. At the helicarrier, Nick Fury states he doesn't need more shellheads flying around, when Andros introduces himself and his wish to prevent S.H.I.E.L.D.'s future crimes. He quickly cripples the Helicarrier. Iron Man and Hawkeye arrive, but Andros' defenses obliterate the arrow before the nanovirus can enter. Rhodey reasons the joints might be Andros' weakest point. Andros attacks the helicarrier again. He lands on the deck, and snaps Hawkeye's shoulder before he can get the last arrow off. He then blows Black Widow up, sending Tony into a rage. Andros disintegrates him with his uni-beam. Hawkeye finally succeeds by firing the arrow into Andros' elbow, and his armor immediately begins to shut down. Black Widow kicks him down. Andros realizes the nanovirus is what will become VORTEX, and that Tony only created it because of his own interference!
Quickly, Andros makes a final timejump to just before he disintegrated Tony. He explains the nanovirus is VORTEX. Hawkeye's arrow is again heading for Andros' elbow, but Tony quickly destroys it. The first Andros fades away, while the second's armor appears to stabilize. Andros scans the future, and can see VORTEX's influence no longer - the future is saved. He disappears, the future being changed so he no longer exists.
Hammer freaks out as the future news article celebrating him as president turns into an article of him as an old man behind bars. Sasha laughs.
- Originally Nicktoons stated "Iron Man 2099" will air before "Ctrl-Alt-Delete", but "Ctrl-Alt-Delete" aired first on March 28, 2012. "Iron Man 2099" will not be broadcast until Summer 2012 after the Avengers live action movie is released in theatres. Despite that, the episode was published on Nicktoons website instead of the next episode.
- Hawkeye and Black Widow team back up though on the hero side instead of as thieves as originally introduced.
- Spider-Man is specifically confirmed to exist in this reality by a Maggia soldier when Hawkeye uses a net arrow who mistakes Hawkeye's net for Spider-Man's webbing. Hawkeye introduces himself as the "Friendly Neighborhood Hawkeye" to them. Black Widow uses the famous Spider-Man line (usually to Doc Ock) "Spiders AREN'T insects". Spider-Man does not appear on-screen.
- Nicktoons has officially stated "Iron Man 2099" will have its TV premiere broadcast on June 6, 2012.