In this incarnation of Iron Man, Tony Stark is a teen who works alongside his brilliant father, Howard, at Stark Industries. After Tony's dad dies, Tony moves in with his friend Rhodey and starts going to school and other teenager-like stuff.
After a plane crash kills Howard Stark and seriously injures his son, Tony, Obadiah Stane takes control of Stark Enterprises. But Tony believes that his father's death wasn't accidental and uses a suit or armor that he invented to gather information from Stane. In the process, Tony saves an out of control train and becomes a public hero by the name of Iron Man.
Obadiah Stane has turned a laser drilling machine that Tony invented for Stark Enterprises into a laser weapon and is trying to sell it to the military. While Iron Man attempts to stop the machines from overloading and exploding during a demonstration, Obadiah Stane is paid a visit by the Mandarin who is looking for something Stane is wearing on his finger.
After Tony is captured by a secret organization, he learns that Gene's father has something to do with it.
Despite Rhodey's reservations, Iron Man builds an alliance with a man named Blizzard. Wanting to take out Obadiah Stane, Tony feels that the new partnership will be beneficial. But is Blizzard all that he seems to be?
When Pepper's father is targeted by arms dealer Mister Fix, Tony must save the day without revealing his secret. However, this task becomes nearly impossible when Mister Fix sends his agent Whiplash after Pepper.
Ivan Vanko, a scientist who was thought to have been left in space two years ago, crash lands in New York City. Alive because of an environmental suit, called the Crimson Dynamo, Vanko seeks revenge on the program that put him in space in the first place- Project Pegasus. It's up to Iron Man to stop Vanko from destroying Project Pegasus.
The pressures of living a normal teenage life and being Iron Man become too much for Tony. Deciding he doesn't need school anymore, Tony quits and focuses on saving the world as Iron Man full time. But when a new villain, called the Living Laser, appears, Tony learns that he has to graduate in order to take over Stark Industries.
Tony sneaks into Stark International to catch a glimpse of the new Stealth Armor. Unfortunately, the building locks down and Tony is stuck inside. With the help of Rhodey and Pepper, Tony must find a way out of the building without revealing his secret identity.
Tony and his friends' search for the ancient Makluan Rings goes awry when the guardians of the Rings, the Dreadknights, arrive.
During the school science fair, Tony is approached by the leaders of an organization known as the Advanced Idea Mechanics. Offering up his help, Tony inadvertantly creates a new enemy, the Controller. With Tony's friends under its control, Iron Man must step in and save the day.
When Obadiah Stane starts acting strangely, Iron Man investigates. It turns out that Madame Masque, a shape shifting villain, was posing as Obadiah and she has a new target: Iron Man. Now, Tony must clear Iron Man's name after the police come looking for him.
Project Pegasus, under the control of Obadiah Stane, creates an upgraded version of the Crimson Dynamo. With it, they capture Iron Man and begin analyzing the suit. After Rhodey and Pepper bust Iron Man out, Tony is ready for revenge. This time, Iron Man takes on the Crimson Dynamo with help from his new upgrade- the Dynamo Buster Armor.
When Tony and Gene find the third Makluan Ring, they argue over what exactly to do with it. Taking matters into his own hands, Gene accidentally unlocks the ring's guardian, Ultimo. Iron Man tries to detain Ultimo, but is forced to deal with the return of the Mandarin as well.
Mister Fix equips Whiplash with a deadly new virus that infects Iron Man's suit. When Iron Man goes online by itself, Tony is stuck inside the suit. Unable to find a way out, Tony fears that he'll never be able to leave Iron Man behind.
When Iron Man tracks Moses Magnum to A.I.M.'s secret headquarters, he meets someone else who's after Magnum, the Black Panther. Thinking they'll be able to work together, Iron Man goes to the Black Panther for help. Unfortunately, Black Panther is only after Magnum and threatens to reveal Tony's secret if he gets in the way.
When the Living Laser threatens the Earth via a space satellite, Iron Man steps in to save the day. Soon, however, Nick Fury and S.H.I.E.L.D. contact Tony and tell him not to interfere. Not knowing who to fully trust, Tony is left feeling unsure of what to do.
When the Ghost comes after Tony, Madame Masque mysteriously steps in to protect him. Fearing that his friends will get hurt, Tony begins to push them away. Unfortunately, the Ghost captures Madame Masque and Tony is forced to call on his friends for help.
When Pepper gets caught up in the middle of a feud between the Tong and the Maggia, the Mandarin calls on an unlikely source for help- Iron Man.
After Tony accidentally creates an evil virus known as Technovore, he believes that it is gone for good. Unfortunately, the virus grows bigger and sets its sights on Iron Man.
Upon retrieving the fourth Makluan Ring, Gene recalls memories of his mother and his birthright. The guardian of said Ring, Firebrand, traps Pepper and Rhodey inside an active volcano and Iron Man must get them out before it erupts.
A.I.M. uses a dying Living Laser to power up their newest creation- the Mental Organism Designed Only for Conquest. When Iron Man can't beat MODOC's mental powers, it's up to the Living Laser to save his life.
After Tony lets Rhodey take the Iron Man suit out for a spin, it falls into the hands of Happy Hogan. Now, Tony must help Hogan take down a Maggia plot, all while not revealing his secret.
The Controller uses a boy named Rick Jones to get the Hulk to take revenge on A.I.M. Stepping in, Iron Man is taken over by the Controller and only the Hulk can stop him.
Obadiah Stane calls on Tony to find a cure for his daughter Whitney's disease. Knowing of a cure that exists in an abandoned Stark facility in the Arctic, Iron Man heads off to find it. Unable to sit around and do nothing, Stane forces Blizzard to go get the cure as well.
Zhang, Gene Khan's father and the former Mandarin, captures Tony and his friends in order to retrieve all five Makluan Rings. When the guardian of the fifth ring is released, the mighty dragon Fin Fang Foom becomes quite a challenge for the gang. Will Tony and Gene be able to save the day without the help of the Iron Man suit or the other Makluan Rings?
Doning the War Machine suit, Rhodey arrives just in time to save his friends from Fin Fang Foom. Now, it's the battle of the century as Iron Man and War Machine face off against Fin Fang Foom and the Mandarin.