The most deadly and dangerous group on the planet, the Cobra organization seeks nothing less than global domination - and it will not rest, will not sleep, until it has achieved its goal.
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Most of what is now the terrorist organization Cobra was originally a covert wing of the weapons company M.A.R.S. Industries, owned by James McCullen. McCullen convinced NATO to fund his Research & Development projects to build more advanced weapons. At the same time, he conceived of an elaborate plan to take over the world: to create an enemy that would inspire fear on a global scale, and make everyone turn to the most powerful individual in the world. To this end, he assembled a small team of specialists and turned M.A.R.S. Industries's virtually unlimited resources to espionage and terrorism.
Among McCullen's operatives was a former U.S. Army Science Officer named Rex Lewis, who eventually evolved into a masked, disfigured scientist known as "The Doctor" and was marked by a fascination with snakes. He was tasked with developing nanomites as weapons, leading to the creation of the nanomite warheads, among other things.
Ultimately, McCullen's plan was thwarted by the anti-terrorist group G.I. Joe, who split up to stop his attacks on the world's capitals and destroy his base in the Arctic. During the battle, McCullen was injured by a flamethrower and escaped with the Doctor in a submarine. The Doctor took this excuse to inject him with a special nanomite solution, which helped to heal his burns, but at the cost of a metallic face -- and the Doctor's complete control over him. The Doctor donned a new mask and declared himself "Commander", using the king cobra as a symbol for what was now his organization, with McCullen as his unwilling lieutenant, "Destro".
Several minutes later, their forces were routed, and both Destro and the Commander were captured by the G.I. Joe. From his cell, the Commander swore to Duke that their battle had only just begun.
In fact, the situation with the nanomite warheads was only part of a bigger plot involving Zartan, a master of disguise. With the aid of a Neo-Viper agent, Zartan infiltrated the White House under the guise of the President of the United States and waited for further orders.G.I. Joe: The Rise of Cobra
Despite the Commander and Destro's imprisonment, the rest of M.A.R.S learned of Lewis's usurpation. M.A.R.S was soon completely rebranded as Cobra and accepted Lewis as their leader.
In the aftermath of the capture and imprisonment of its two largest leaders, Cobra lies low for a time, carrying out its plans only in secret in order to allay suspicion. Zartan rules from the White House as the false Preisdent, pursuing a more aggressive military stance, but otherwise initially avoiding making any overt moves that would draw attention.
Things change when the President of Pakistan is killed in a terrorist attack. Zartan seizes the opportunity, sending in the G.I. Joe Team, now led by Duke, to seize Pakistan's nuclear weapons before they can fall into the hands of one of the several competing warlords that are vying for control of the nation. The mission, however, is a setup, as upon learning of its successful completion, he sends in an airstrike intended to annihilate the G.I. Joe Team. Duke is killed in the attack, leaving Roadblock as the team's leader. Zartan then tortures the President for the location of the secret underground prison where Cobra Commander and Destro are being held.
Storm Shadow infiltrates the secret prison, disguised as his enemy, Snake Eyes. He allows himself to be captured and placed into stasis in a water tank, only to use a trick to slow his heart-rate to catch the prison's wardens off-guard and break free. With assistance from Firefly on the outside, he succeeds in rescuing Cobra Commander. He then turns his attention to Destro, but Cobra Commander stops him, telling Destro "Sorry, Destro, you're out of the band."
Cobra Commander, Destro and Storm Shadow meet with Zartan, who is disappointed to learn that most of the G.I. Joes survived. Nevertheless, they proceed with their new plan: Project Zeus. Zartan returns to the President, this time with Cobra Commander, and they force him to submit to a retinal scan in order to unlock the briefcase that controls America's nuclear arsenal. Zartan then announces a summit at Fort Sumter with the leaders of the world's nuclear nations. Lady Jaye, one of the G.I. Joe agents, sneaks into a dinner celebrating this summit and obtains a hair sample, getting Zartan's DNA and proving that he is the President. She and the other members of the team then launch their own plan to act based on their belief that Cobra's objective will be revealed during the summit.
At the summit, Zartan meets with heads of the world's other nuclear nations, telling them that his goal is total nuclear disarmament. When they object to this idea, he tells them they will all be at war with America if they do not accede to his demands, then when they continue to protest, he launches America's nuclear arsenal. In response, they set off their own warheads, only for him to suddenly cancel America's attack, telling them that they need to cancel their own if they don't want to be blamed for a tragedy. They do so and then Zartan puts up images on a monitor, telling them that they're looking at images of their homelands. He then reveals something called Project Zeus, explaining that it's a new weapon that can be dropped quickly from orbit without any fallout and demonstrates by dropping it on London, devastating the city.
Cobra Commander then takes over, telling the remaining world leaders that the price for not having their homelands' capitals destroyed also is total allegiance. Before he can continue, however, G.I. Joe begins their assault, led by Storm Shadow, who has learned the truth that it was Zartan who framed him for killing the Hard Master. He succeeds in killing Zartan, while Lady Jaye and General Joe Colton rescue the President. Roadblock, meanwhile, secures the case controlling Zeus from Firefly and manages to shut it down before killing him. In the melee, however, Cobra Commander manages to escape, remaining at large.G.I. Joe: Retaliation