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. - File card.
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. While McCullen built up his company and convinced NATO to fund his Research & Development projects to build more advanced weapons, motivated by his family's heritage, 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 MARS' 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 (named for his ancestor) as his unwilling lieutenant, "Destro".
Several minutes later, their forces were routed, and both Destro and the Commander were captured by the U.S. military. 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 was last seen waiting for further orders.
Despite the Commander and Destro's imprisonment, the rest of M.A.R.S learned of Rex Lewis usurping McCullens organisation. So by the events of G.I. Joe: Retaliation, M.A.R.S was completely rebranded as Cobra and accepted Rex Lewis as their leader.
Cobra had suffered by two defectors to Joes: When Ana who is sister of Rex injected her as Baroness had turn against her brother and James after her love for Duke overcome her darker side and her teacher Storm Shadow help Joes exposed to Cobra as terrorist and kills Zartan after he learning that Zartan was framed him for Hard Master's death.