- An elite military unit comprised of special operatives known as G.I. Joe, operating out of The Pit, takes on an evil organization led by a notorious arms dealer.
- Two soldiers stationed in Kazahkstan (Captain Duke Hauser and his partner "Ripcord") are ordered to transport special warheads created by MARS, an arms' manufacturer controlled by James McCullen. When they are attacked by thieves (led by Anastasia DeCobray, with whom Duke has history), they are saved by a top secret, international special forces unit known as "G.I. Joe". The leader of G.I. Joe, General Abernathy (or Hawk) is on the trail of the thieves: an evil organization called "Cobra". While Duke and Ripcord train to join the Joes, McCullen ("Destro") is secretly working for Cobra and plotting to recapture his metal-eating "Nanomite" warheads. Duke and Ripcord (with help from Heavy Duty, Snake Eyes, and the rest of the Joes) must prove that they are Real American Heroes -- by stopping the launch of these warheads before Cobra uses them to take over the world.—John Wiggins
- In the past the McCullen's were arm makers and supplied both sides in a war. A McCullen ancestor was caught and was imprisoned in France with an iron mask on his face to teach all his future generations not to repeat this crime. McCullen vows that clan McCullen will run future wars, not just supply them.
In the near future, weapons master James McCullen (Christopher Eccleston) (A weapons designer and the founder of M.A.R.S.) has created a Nanotech-based weapon-Nanomites designed to devour metal and other materials, capable of destroying anything from tanks to cities. The nanobots can only be stopped by activating the kill switch.
His company M.A.R.S. sells four warheads to NATO, and NATO troops led by American soldiers Duke (Channing Tatum) and Ripcord (Marlon Wayans) are asked to deliver the warheads. Their convoy is ambushed by the Baroness, whom Duke recognizes to be his ex-fiance Ana Lewis (Sienna Miller) (The sister of Cobra Commander and a spy). The Baroness has futuristic weapons, and the NATO arms are no match for them, it's a massacre.
Duke and Ripcord are rescued by Scarlett (Rachel Nichols) (Scarlett graduated from college at age 12 and became the team's intelligence expert), Snake Eyes (Ray Park) (A mysterious ninja commando who took a vow of silence), Breaker (Said Taghmaoui) (The team's communications specialist and hacker), and Heavy Duty (Adewale Akinnuoye-Agbaje) (An ordnance expert and field commander of the team). Anna and her forces retreat.
They take the warheads to The Pit, G.I. Joe's command center in Egypt, and upon arriving, rendezvous with the head of the G.I. Joe Team, General Hawk (Dennis Quaid). Hawk takes command of the warheads and excuses Duke and Ripcord, only to be convinced to let them join his group, after Duke reveals that he knows the Baroness. Hawk asks McCullen to open the weapons case via Telepresence, but in doing so, McCullen activates its tracking device.
McCullen is revealed to be using the same nanotechnology to build an army of soldiers with the aid of the Doctor (Joseph Gordon-Levitt) (The Baroness's brother, a former soldier who was thought to have been killed during a mission led by Duke-instead he survived the attack, but he became the disfigured head scientist of Military Armament Research Syndicate (M.A.R.S.)), planning on using the warheads to cause worldwide panic and bring about a new world order. The super soldiers have Nanomites injected into them and feel no pain and can eject harmful particles like poison and can self-heal the body during battle.
Using a tracking device, McCullen locates the G.I. Joe base and sends Storm Shadow (Byung-Hun Lee) (Snake Eyes's rival; both were close members of the Arashikage ninja clan) and the Baroness to retrieve the warheads, with assistance from Zartan (Arnold Vosloo) (A disguise expert who serves Destro). They infiltrate the Joe stronghold via mole pods that burrow underneath the desert. But the pods are destroyed by Joes during battle. After a fight, Storm Shadow and the Baroness retrieve the warheads (They escape by using the single person jet propulsion kits) and take them to Baron DeCobray (Gregory Fitoussi), the Baroness's husband, for him to convert them into weapons in his particle accelerator; after he reluctantly does this, DeCobray is killed by Storm Shadow.
Making their way to Paris (McCullen wants revenge on the French for making his ancestor wear the iron mask all those years ago), the Joes pursue the Baroness and Storm Shadow (They figured that McCullen stole his warheads backs and they know Anna is married to a French scientists who runs a particle accelerator lab that can be used to turn the warheads into weapons) (The Joe arrive just as Anna and Storm Shadow are leaving Decobray's lab), but are unsuccessful in stopping them from launching one of the missiles. The missile hits the Eiffel Tower and releases the Nanomites in it, destroying the tower and some of the surrounding area before Duke manages to hit the kill switch which was with Anna (who was escaping in a helicopter). However, in doing so, he is captured and taken to McCullen's base under the Arctic.
A brief history on Storm Shadow and Snake Eyes. Storm Shadow was a Korean pupil at his Japanese master's temple. Snake eyes entered later as a wastrel, but master takes him in as Snake Eye fights like a champ. Storm Shadow beats Snake Eyes in early rounds of practice but the master never praises him as he sees blackness in his heart. When Snake eyes starts to win, master praises him, angering Storm Shadow, who kills the master and escapes.
The Joes locate the secret base (Duke turns on the same tracking beacon on the case that McCullen did) and fly there, as McCullen loads the three remaining warheads onto three missiles, which are aimed for Beijing, Moscow, and Washington, DC, the world's three most important capitals. He states that he intends to do this because by killing millions of people in these cities, he will strike fear into the hearts of every man, woman, and child on the planet, after which they will turn to the person with the most power in the world, the President of the United States.
After Snake Eyes takes out one missile with a jet ski missile, Ripcord destroys the remaining two by using a stolen M.A.R.S. prototype Night Raven jet, while Scarlett, Breaker, and Snake Eyes infiltrate the base. Snake Eyes duels and prevails over Storm Shadow. Duke learns that McCullen's employer the Doctor is actually Rex Lewis, Ana's brother, believed to have been killed by a mistimed airstrike during a mission led by Duke (also the origin of the alienation between Duke and Ana). Rex says how he had encountered Dr. Mindbender (Kevin J. O'Connor) in the bunker and was seduced by the Nanomite technology, taking too long to retrieve the data and getting caught in the bombing, which disfigured him.
After freeing Duke (she is able to break through the mind control of the Nanomites and realize that she really loves Duke), the Baroness is subdued, as the Doctor reveals he has implanted her with Nanomites, which has put her under his control for the past four years. Attempting to kill Duke using a flamethrower, McCullen ends up being burned when Duke shoots the weapon and causes it to explode, so Rex and he flee to an escape vessel. Duke and the Baroness pursue him while the Joes fall back; when Rex activates the base's self-destruct sequence, which involves 'blowing the ice cap' to create blocks of ice which then nearly crush the Joes.
Rex assumes the identity of the Commander, having healed McCullen's burned face with Nanomites, transforming his skin into a silver-like substance and naming him "Destro", which places McCullen under the Commander's control. They are captured by G.I. Joe soon after. On the super-carrier USS Flagg, the Baroness is placed in protective custody until they can remove the Nanomites from her body.
Meanwhile, Zartan, having had his physical appearance altered by Nanomites, infiltrates the White House during the missile crisis and assumes the identity of the President of the United States, thus completing a part of McCullen's plan to rule the world.
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