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Cobra Commander managed to track Snake-Eyes to Japan, where he was training to become a member of the Arashikage ninja clan. The Commander hired a mercenary called Firefly to kill him, but Firefly soon realized he was no match for his target, instead referring Cobra Commander to another assassin, Zartan, who infiltrated the clan and shot at Snake-Eyes with an arrow stolen earlier from another ninja, Storm Shadow. However, it was not Snake-Eyes who was hit, but the clan's leader and Storm Shadow's uncle, Hard Master. Storm Shadow was blamed for the murder and fled in search of the killer.
Cobra Commander returned to his domestic life, but after his wife gave birth to a son, Billy, she found out about what had happened in Japan. He took the child and left his wife, becoming increasingly paranoid and blaming all his problems on "the system." He traveled across America with Billy, seeking out people who shared his desire to topple big business and the government, using money he had earned from pyramid schemes to attract followers.
He then moved to the town of Springfield, where the businesses were struggling and the population had become disillusioned with existing policy. He applied his influence to corrupt the township and eventually took control of it. Within the town, he established a clandestine terrorist group called Cobra. For reasons and in ways unknown, Billy left his father and joined the anti-Cobra underground organization. Storm Shadow's search for his uncle's killer eventually led him to Cobra, which Storm Shadow joined, pledging loyalty to Cobra Commander as his personal bodyguard.
For a long time, Cobra remained a clandestine organization, slowly building up its forces and resources. Cobra Commander finally initiated a bold plan by kidnapping renowned nuclear physicist Dr. Adele Burkhart. The U.S. government responded by sending in the G.I. Joe Team to rescue her. Scarlett and Snake-Eyes managed to infiltrate the base and reached him holding Burkhart hostage. Burkhart tried to sacrifice herself to save the Joes. Scarlett injured the Commander but he managed to escape.
Irked at the Joes' interference, Cobra Commander initiated a plan to let a sophisticated battle robot be captured by the Joes. The robot was meant to be transported to the Joes' headquarters, the Pit, where it will activate by itself, attempt to escape and beam the Pit's location. The Joes caught wind of the plan and it failed. Hoping to get a piece of G.I. Joe technology, the Commander initiates a plan to capture the M.O.B.A.T. during an Armed Forces Day parade. Even without ammo, the Joes proved resourceful enough and his command post was exposed. General Flagg almost had him but he was able to use a hostage and make good his escape. He also proved his ability to manipulate those not directly under his control as he let the Joes and the Oktober Guard fight over a spy plane and then had them surrounded and take the prize away. Despite, his flair for a theatrical appearance, he is not a fool to deliberately put himself in danger as the G.I. Joe member named Clutch took hostage a robotic doppelganger instead.
The Baroness and Major Bludd recruited Billy to carry out Cobra Commander's assassination, but he was intercepted by Destro before he could accomplish his task. Cobra Commander had become such a rabid megalomaniac by this point that he had no qualms about torturing his own son, yet Billy refused to surrender any information identifying who had sponsored the hit. Such tenacity impressed Storm Shadow, so he freed Billy and they both escaped to New York, where Storm Shadow trained him in ninjitsu. Billy was later caught in the crossfire between the Soft Master and Cobra agent Scrap-Iron, when the car he was driving in exploded.
Cobra Commander ordered the creation of a new genetic lifeform - a super soldier who combined DNA from many of history's greatest warriors. The new being called Serpentor was created just as the G.I. Joe Team attacked Springfield. However Serpentor proved more than just a warrior but also a charismatic leader and skilful politician whose charisma in battle won him a strong following amongst Cobra troops. Cobra Commander ordered Zartan and the Dreadnoks, who always remained loyal to him, to assassinate Serpentor disguised as members of the G.I. Joe Team, but Serpentor survived and used the incident to seize the initiative and demand an attack on the Joe base, the Pit, despite Cobra Commander's misgivings.
The attack was militarily a success but also saw Cobra Commander and Serpentor continue their conflict, with each trying to seize the advantage over the other. As a result Cobra Commander and Destro ventured underground at personal risk and were trapped when the Joes destroyed the base to save secrets. Cobra Commander and Destro were trapped underground, presumed dead. However they survived and were forced to work together to make their way to freedom. Given the danger of Serpentor, they undertook to keep a low profile as they made their way home. It was during this cross-country trek with Destro that Cobra Commander learned of Billy's fate: though he survived the explosion, he had lost a leg and an eye, and lay in a coma ever since. Unnerved by the tragedy, the Commander took responsibility for Billy's condition, and promised to be a better father. Seeking out the Crimson Guard Fred VII, a mechanical genius who built Billy a new robotic leg, the Commander set up shop in Denver, where Billy eventually awoke from the coma. Fitted with a mechanical prosthetic leg by Fred VII, Billy unwittingly stumbled upon the Blind Master and Jinx. Seeing that Fred VII had constructed a suit of battle-armor for Cobra Commander, who was once again plotting to take over the world, Billy walked out on his father. The incident left Cobra Commander to reflect on the folly of his ways, but Fred VII was so angered to see his commander throwing away what he had dedicated his life toward that he shot Cobra Commander in the back, apparently killing him.
Unaware that he was being watched, Fred VII buried the body. It was exhumed by another Crimson Guardsman, Fred VIII, who discovered that Cobra Commander was not dead after all, and managed to revive him. With Fred VII masquerading as him in Cobra, the Commander began to form a new organization in secret. When Dr. Mindbender went to Cobra Commander's supposed grave to harvest DNA for the genetic creation of a new leader, he instead discovered the empty grave.
Cobra Commander took that opportunity to return to Cobra, this time even more maniacal than before, filled with rage and unwilling to harbor any traitors (real or perceived). His first act was to imprison those who had betrayed him: Fred VII, his partner Raptor, Firefly, Dr. Mindbender, Zartan, Billy, and numerous Cobra troops, all of whom he had buried alive within a volcano on Cobra Island. He relinquished all traces of morality and humanity, and rebuilt a new command infrastructure by instituting a brainwashing program to compel allegiance from those around him, including repeatedly brainwashing Destro, The Baroness, Zartan, Storm Shadow and Billy. He also became much more willing to kill, even personally executing Borovian rebels Magda and the White Clown.
(info from G.I. Joe Wiki)
Battle vs. Red Skull (Comics) (by Thundrtri)Edit
No battle will be written
Winner: Cobra Commander
Cobra Commander won because his weaponry and tactics were more advanced. The HISS tanks also proved more efficient in combat than the HYDRA tank.