Inventor Howard Stark seemingly dies in a plane crash while investigating an ancient Chinese "Makluan ring". His son, Tony Stark, barely survives the crash when the armored exoskeleton-battle suit which Tony designed and built himself implants in his chest a device to sustain his damaged heart. Obadiah Stane takes control of Howard's company, Stark International, and begins weaponizing Stark's inventions. Tony moves in with family friend James "Rhodey" Rhodes and his mother, Roberta, and begins attending school. There, he meets classmate Pepper Potts who informs Tony that Stane is under investigation by the FBI for possible involvement in Howard's supposed death. When Tony goes to investigate in his armored battle suit, he ends up preventing a runaway train from crashing into Stark Tower; the media calls him Iron Man. A shadowy figure called the Mandarin, wearing a second mystical Makluan ring, vows to obtain the second ring now in Stane's possession.

The Mandarin, shown to be an old man named Zhang, quarrels with his stepson Gene Khan. When Stane demonstrates his weaponized version of Tony's "Earth Mover" invention to a group of potential buyers, Tony, as Iron Man, destroys them. Meanwhile, Gene, having imprisoned Zhang, appears as the Mandarin and takes Stane's ring.

As tensions mount between the Tong and rival criminal organization the Maggia, Gene enrolls in the Tomorrow Academy to be closer to Tony in hopes of learning more about the Makluan rings. When a team of Maggia thugs headed by Unicorn and Killer Shrike kidnap Gene, Tony, and Pepper, Rhodey remotely pilots the Iron Man armor to their rescue.

In hopes of exposing Stane as evil, Tony teams up with Blizzard, until he realizes that Blizzard wants to hurt Stane along with anyone else who gets in his way. As Iron Man, Tony reluctantly saves Stane, leaving Blizzard cryogenically frozen in Stark Tower.

Tony is still flunking school and is placed in the lead role of Hamlet (which ironically mirrors his situation). He learns from a holographic will of his father that he wanted him to have a normal life rather than letting the company be a burden on him. However, a Maggia member named Arthur Parks becomes the Living Laser through use of an experimental vest stolen during a raid. Iron Man is able to stop him and remove the vest but it had a lasting effect on the Laser, whose body turned to pure energy and resolves to take down Iron Man.

Rhodey becomes concerned over Tony's plans to increasingly weaponize the Iron Man armor using reverse engineered captured tech. Obadiah Stane offers to bail out Anton Harkov and Project Pegasus in return for the Crimson Dynamo armor which is upgraded to capture Iron Man, resulting in a pitched battle in the middle of the city that leaves Stane furious at the reckless endangerment of innocent lives. Having lost the battle and fallen unconscious, Tony is brought to Project Pegasus. Harkov and Stane then begin to analyze the Iron Man armor. With the help of Rhodey and Pepper, Tony manages to escape, only to return in the Dynamo Buster armor (which resembles the Hulkbuster Armor). He then uses a virus called 'Technovore' to destroy Pegasus' advanced AI Delphi, both to defeat the Dynamo and prevent Stane from acquiring detailed technical data on Iron Man. Tony is excited that he finally defeat one of his enemies, saying that what they need to win is better tech, weapons, and to stay ahead. Rhodey, on the other hand, reminds Tony that there is a line between good and evil, and that he just came close to crossing it. Though successful, there is an unexpected consequence, back at Project Pegasus having consumed all available data, the Technovore is close to burning itself out just as Tony planned. When Obadiah Stane is informed by his secretary that Anton Harkov is on the other line, Obadiah has her tell Anton Harkov that the offer is rescinded. But unknown to Tony one of Pegasus' projects were computer-controlled nano-mites. Using the connection Technovore takes control of the Nano-mites abandoning the computer, it forms a body and says one word "Consume".

The Technovore virus that Tony unleashed against Project Pegasus didn't burn out as intended. It has acquired the nanotechnology and is running loose in the Project Pegasus complex, assimilating any technology it can gets its hands on. It has taken on the shape of a robot, which bears resemblance to Spider-Man villain, Carnage. Meanwhile, Nick Fury sends some S.H.I.E.L.D. Agents to bring Tony to repair the S.H.I.E.L.D. Helicarrier's engines. It is also revealed that the Living Laser is dying and that S.H.I.E.L.D. intends to let him waste away as he was a villain. Rhodey goes to the Pegasus facility to check out a disturbance only to run into Technovore, when it gets a hold of Rhody's earpiece, it calls Tony so it can absorb the Iron Man armor. After the Pegasus scientist who was hiding in the building fled, Tony arrives. After exhausting every option, Tony activates the armor's self-destruct sequence, and abandoned the armor and ran for it. The explosion destroys both Technovore and the facility. Meanwhile somewhere in Russia, Anton Harkov leaves a plane. But unknown to him, a microscopic cell of Technovore's nanomite body still remains inside the fabric of his coat.

When Tony responds to the Hulk's rampage in the Dynamo Buster armor, the Controller takes control of him to attack AIM. The Controller had been manipulating Rick Jones, friend of the Hulk, to the same end. The Hulk agrees to help save Iron Man, and finds him at AIM headquarters struggling against the Controller's attempts to force him to kill the wounded MODOC, whose mental attacks are powerless against a mind under the Controller's power. Hulk liberates Iron Man by destroying the controller disc. MODOC escapes, the Controller passes out, and Rick and the Hulk move on.

When Stane builds duplicates of the Iron Man armors called the Guardsmen (consisting of Force, Shockwave and Firepower), Tony must reveal they are frauds. But this causes the civilians to start hating Iron Man, as they believe that he is simply jealous of the town's new heroes.

Note #1: Pepper's crush is made obvious to Tony when in the lab Tony says "Pepper I could kiss you" and her response is "What is stopping you?" she blushes and Tony never responds. This displays the possibility of perhaps a new relationship in bloom in which Tony and Pepper begin to date.

Several attacks on Hammer Multinational lead Tony to discover that Stark International is involved in a civil war. Iron Man discovers that Black Panther is back and is targeting Justin Hammer.

Note: Pepper mentions Iron Fist.

With Justin Hammer finally acquiring specs from the Iron Man armor, he presents potential weapons buyers including Nick Fury with his new creation: Titanium Man.

Obadiah Stane forms an unlikely partnership with Doctor Doom in a plot to claim the Iron Man armor. Unfortunately, Doctor Doom has plans of his own for Iron Man, and his seemingly magical powers seem too much for Iron Man to handle.

Iron Man attempts to stop Hawkeye and Black Widow from stealing Stark Internationals' UI Chip. As a result, Justin Hammer uses the rebuilt Titanium Man armor to steal the UI Chip and the three must reluctantly team up to get it back.

Note #1: Pepper mentions a "Boxing Glove Arrow" This is used by DC comics Green Arrow. A marksman like Hawkeye.

Black Widow returns stealing from Nick Fury and the S.H.I.E.L.D. helicarrier, and by circumstance and some cold calculation Iron Man ends up being hunted by S.H.I.E.L.D. for that deed.

Note #1: Reed Richards is specifically mentioned as a featured lecturing scientist (though he does not appear on camera). No specific mention of the Fantastic Four is made.

Note #2: The vibranium-adamantium alloy is specifically introduced in this episode. Originally this alloy was stated to be the secret metal compound of Captain America's "indestructible" round shield before the shield was retconned to being only vibranium and iron. No specific mention of Captain America is made.

Schoolmate Rhona Irwin turns Tomorrow Academy into a lethal maze of traps for Tony and his schoolmates while her twin brother Andy turns out to be very unexpectedly lethal as well. Now Tony must survive Rhona's D.A.T.s (short for Deadly Aptitude Test), free Pepper, Rhodey, Happy, and Whitney, and get to his Iron Man armor to defeat Rhona and Andy.^[25]

After the events involving the Iron Monger armor, Obadiah Stane begins to have it mass-produced. With footage discovered by Tony Stark and Roberta Rhodes which involved his deal with Ghost, Obadiah Stane is fired by the Chairman of the Board. Unfortunately, a comment from Tony accidentally reveals Iron Man's real identity to Obadiah.^[27]

Note #1: General Thunderbolt Ross is introduced. Ross buys the vibranium-adamantium alloy coated Iron Monger robot as "part of the biggest military contract in history".

Note #2: Stark mentions that there are "other heroes" when he decides to retire from being Iron Man. These other heroes are not specifically identified.

Justin Hammer manages to buy Stark International, much to the disappointment of Tony Stark. As Iron Man, Tony plans to expose Justin Hammer's true nature. This won't be easy since he'll have to go through Killer Shrike, Unicorn, Whiplash, and even Titanium Man to do so. In the end, even though Hammer owns Stark International, Tony Stark decides to create his own company called Stark Solutions.

Note #1: At the beginning of the episode, Blizzard travels by creating "ice slides" to ride on which are almost identical to Iceman.

Note #2: When Justin Hammer bombards War Machine with artificial cosmic waves, the possible effects he suggests (hardening like a statue, bursting into flames, melting into a puddle of goo, or vanishing into thin air) are nods to the Fantastic Four.

When S.H.I.E.L.D. Agent Mallen is fired by General Nick Fury, Mallen takes the super-serum "Extremis" and mutates into a powerful maniac bent on revenge. When Iron Man tries to fight Mallen, he ends up defeated and in critical health ... and his only salvation would be a dose of the selfsame Extremis. However, the serum not only repairs his heart, but also gives him brand-new technopathic powers, now becoming one with his armor, and faces Mallen.

Tony's new friend Annie Claremont turns out to be a mutant on the run from Magneto (who wants to use her to assassinate anti-mutant politician Senator Robert Kelly). Iron Man tries to protect her, but how can he fight a mutant with a mastery over all things metal?^[34]

Tony gets an unexpected visitation from his future grandson Andros, who has come to eliminate Tony Stark, since he believes that by designing a super-virus named 'Vortex', Tony will be responsible for a catastrophe in the year 2099.^[36] Now Tony must take down his own futuristic grandson with the help of Hawkeye, Black Widow, and S.H.I.E.L.D. while avoiding the future disaster at the same time!

Note #1: 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" did not broadcast until Summer 2012 after the Avengers live action movie was released in theaters.^[37] Despite that, the episode was published on Nicktoons website instead of the next episode.

Note #2: Hawkeye and Black Widow team back up though on the hero side instead of as thieves as originally introduced.

Note #3: 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.

Tony wakes up in the Mainframe, a virtual world created by the Controller in a plan to enslave the city – but to reach his goal, he needs Tony's Extremis powers.^[40]

Note #1 : Nicktoons broadcast "Ctrl-Alt-Delete" before "Iron Man 2099", contrary to previous scheduling.

To keep reality itself from being torn apart, Iron Man must team up with The Mandarin to stop Doctor Doom after he captures the Ninth Makluan Ring ... and his father Howard Stark.

Note #1: The guardian in the Ninth Temple is the Grey Gargoyle, though with him having been destroyed by Doctor Doom, he makes no actual appearance in this episode.

Note #2: This is the first episode where Pepper actually dons an Iron Man suit to fight alongside Rhodes against wormhole predators from another dimension.

To keep Stark International from being re-purchased by the Starks, an increasingly insane Justin Hammer unleashes Titanium Man on his former henchmen (whom he suspects to be blackmailing him to give up Hammer Multinational) and develops a sinister zombie gas as his latest weapons project!

Note #1: Roberta Rhodes mentions a court case called "Lieber Vs. Heck", which is a reference to Stan Lee (aka Stanley Lieber) and Don Heck, the creators of Iron Man.

Note #2: Attorney Matt Murdock is specifically mentioned in this episode. Murdock does not appear on camera.

Fugitive scientist Bruce Banner seeks out the Starks for help to rid himself of the Hulk. But when army soldiers led by General Thunderbolt Ross co-opts S.H.I.E.L.D. to make an attack, Iron Man must fight and subdue the Hulk to save him!

Note #1: Bruce Banner shows up on screen for the first time. This episode also features Glenn Talbot as a S.H.I.E.L.D agent, and Rick Jones makes a cameo appearance.

Note #2: Hulk changes into the more intelligent Grey Hulk at the end of the episode.

Obadiah Stane and Iron Monger apparently return to wreak revenge on Tony Stark by poisoning Howard, but it is actually a mentally unstable Madame Masque, who is seeking revenge for Tony rendering Obadiah comatose.

Just a few days before his eighteenth birthday, Tony, Rhodey, and Pepper in her brand new battlesuit travel to China to search for the Mandarin. Gene finds the tenth ring and defeats the last guardian, but the rings - and Gene - harbor a deadly secret. In the meantime, Tony is confronted with the need to tell his father a very important truth ...

Note #1: Pepper's Rescue armor is dark purple and white, instead of red and white as in the comics.

Note #2: Pepper mentions the Invisible Woman.

Just on Tony's birthday, the Mandarin makes his move and demands domination over the world. But things take a surprising turn for the worse when the Makluan Overlord arrives on Earth in their spaceship to reclaim the Makluan rings and start a full-scale invasion. Now Tony, Rhodey and Pepper have to save the world and battle the Makluan aliens with Mandrin(without rings).

Note #1: Mandarin teleports the SHIELD Helicarrier to the Negative Zone. General Fury and Black Widow is left on the ground.

Iron Man's friends and allies unite against ultimate odds to prevent the utter destruction of the Earth at the hands of the Makluan Overlord.

Note #1: Pepper attempts to tell Tony her true romantic feelings towards him, but keeps getting interrupted. Near the end, Tony interrupts her again only to kiss her on the cheek and hug her.

Note #2: The identity of Rescue, Iron Man, and War Machine are revealed to the world.

Note #3: The team made in this episode is similar to that of the Avengers from the 2012 movie: Hawkeye, Hulk, Iron Man, Black Widow. The difference is that Nick Fury and Black Panther replace Captain America and Thor.