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Cobra is a ruthless terrorist organization determined to rule the world!
They sometimes team up with or rebuild Transformers.
While nothing is stated outright, it appears that the threat of mighty Cobra is now but a memory.
Among the other members of the Concurrence was Count von Rani, who himself clashed with Sgt. Savage as Iron Klaw, but who otherwise has no known connection to Cobra.
Marvel Comics continuity
G.I. Joe And The Transformers
Cobra manipulated Senator Barbara Larkin, using her to push through the development of Power Station Alpha so that they could then steal it for their own purposes. Things went awry when the Decepticons decided they wanted it for their own, but an alliance was soon formed... and broken, when Cobra learned the Decepticons planned to use Alpha to destroy the world.
G.I. Joe Starring Snake-Eyes and the Transformers
In the midst of a scheme by Cobra Commander to bring new glory to his organization, the reconfigurable Silent Castle he had seized from Destro was put into a state of constant metamorphosis. This caught the attention of a heavily-damaged Megatron, who flew to Trans-Carpathia from Canada and was enraged to discover a non-sentient piece of architecture instead of another Transformer.
This confrontation eventually led to an agreement between Megatron and Cobra whereby Megatron would receive a new, more powerful body (designed by Dr. Biggles-Jones) in exchange for the technologies of the downed-but-functional Autobot Ark.
Cobra helicopters led Megatron and the unearthed Ark from Canada to the Cobra-controlled town of Millville, New York, where its brainwashed denizens began to unload the spacecraft. Their operation was discovered by the G.I. Joe team, who Megatron was vocally uninterested in battling.
Not too long afterwards, a group of Autobots (Brawn, Chase, Hot Spot, Override, Skydive, and Steeljaw) arrived and battled Megatron in Millville, causing considerable damage to Cobra's property holdings and destroying any vestiges of the town's use as a secret base.
As the situation continued to degrade, Cobra Commander ordered an evacuation of the town's assets and personnel from a position near the Ark. Megatron then arrived, and having captured Dr. Biggles-Jones, abruptly disregarded his previous agreement with Cobra Commander. He took the Ark for himself and blasted off, much to Cobra Commander's extreme annoyance.
In-transit, Megatron voiced that he had transferred a virus that had been implanted in his new body by Dr. Biggles-Jones to the Cybertronian technology in Cobra's possession, which would render it inoperable.
Transformers Generation 2
The convoy was assaulted by Autobot Hot Spot, who feared the havoc that could be created by the alien technology in Cobra's hands. As Cobra soldiers prepared to retaliate against him, they were cut down by Snake-Eyes and General Hawk, which gave Hot Spot the opportunity to destroy the transport.
Surrounded and heavily damaged, Hot Spot destroyed himself rather than be captured and dissected by Cobra's technicians for knowledge.
Operatives involved in this mission included Cobra Commander.
Dreamwave comics continuity
In 1938, Major Sebastian Bludd discovered Megatron and his Decepticons in a shrine in the Fera Islands. Soon Megatron allied himself with Bludd's master, Cobra Commander, and they joined forces to conquer Europe. Even the mighty Maginot Line could not stop them as they rolled through Berlin, Paris, and Rome and enslaving their inhabitants. Before long, the Decepticon/Cobra onslaught reached Great Britain.
However, treachery from Destro, the Baroness, and Starscream led the newly-formed G.I. Joe team to their Terrordrome. While engaging Cobra troops commanded by Storm Shadow, the Joes encountered the Autobots, who soon repaired and revived themselves. The Joes soon found themselves under fire from a squadron of Rattlers and Seekers led by Wild Weasel, but they were driven back by Lady Jaye and the Aerialbots.
As this transpired, Megatron attempted to dispose of his insufficiently-efficient human partners, but was humbled by a Matrix-bearing Cobra Commander.
While the Cobra aircraft were driven off, they left behind paratroopers and Rumble. The Joes managed to defeat the troops, and Bumblebee and Scarlett destroyed Rumble, but Zartan managed to murder and replace Breaker in the confusion. He was quickly discovered, but not before he allowed Soundwave to capture Flint.
Storm Shadow left the main Cobra force to engage in a deadly duel with his sword-brother Snake-Eyes, now a member of G.I. Joe. Despite the intervention of Ravage, Snake-Eyes defeated Storm Shadow, who was then eaten by a shark.
Soon, Cobra prepared to defend the town of Torhavn against the approoaching Autobots and Joes, using slaves as human shields. Another Cobra air attack was foiled by Lady Jaye and Superion, leading to the death of Wild Weasel, and Lady Jaye defeated Bludd and the Dreadnoks. Meanwhile, a small Joe strikeforce infiltrated the Terrordrome, destroying Frenzy in the process.
As the Joes, Autobots, and an Allied fleet neared, Shockwave destroyed Superion and a number of ships, damaging himself severely in the process. But despite heavy losses, the Autobots soldiered on.
Destro and the Baroness took advantage of the chaos to unleash their monstrous creation Bruticus upon both sides - but not before slaying their co-conspirator, Starscream. Bruticus' attack crippled Cobra Commander, allowing the Baroness to execute him with Megatron's pistol form. Her victory was short-lived - before the Commander's body could cool, she and Destro were arrested by Scarlett and Snake-Eyes. As the metal monster tore through the Autobots, Snake-Eyes took the Matrix from the Commander's corpse and destroyed it, killing the Autobots, Decepticons, and Bruticus and ending the threat of Cobra.
Transformers/G.I. Joe: Divided Front
Some 45 years after the conquest of Europe, Cobra rose again. Under the command of Cobra Commander, Cobra established extensive operations in the United States. In 1985, G.I. Joe attacked a Cobra shipping facility commanded by Destro. While the facility was largely destroyed, Destro and Scrap-Iron managed to escape via Trouble Bubble. Soon afterwards, Cobra detected the crash of an Autobot shuttlecraft near Portland. Their retrieval force was repelled by a team of G.I. Joe rookies.
[Note: As Dreamwave went bankrupt after only one issue of this series was published, it is unknown whether Cobra Commander and Destro are in any way related to their 1930s counterparts.]
Devil's Due comics continuity
G.I. Joe vs. the Transformers
The fledgling terrorist organization Cobra discovered the Ark and its Transformer crew in stasis lock, and took them to their headquarters on Cobra Island. With the help of mad scientist Dr. Mindbender and weapons dealer Destro, they turned most of the Transformers into remote-controlled war machines - with the exception of Megatron, who was kept by Cobra Commander as a trophy, locked in pistol mode. They were used to strike at a United Nations summit in Washington, D.C., causing mass panic.
Despite problems reprogramming some units (especially Optimus Prime), Cobra launched an attack on the SPS Research Facility. While several of Cobra's Transformers were destroyed in the attack, thanks to the intervention of the newly-formed G.I. Joe as well as two escaped Autobots, Bumblebee and Wheeljack, Firefly managed to acquire the satellite technology and destroy the facility. Their success was short-lived, however, as Cobra's Transformers overrode their programming en masse and rebelled against their masters. Cobra Commander was forced to unleash Megatron to battle Optimus Prime as he attempted to flee. As Cobra troops were slain left and right, the Commander and several other oficers managed to secure S.N.A.K.E. suits and fight their way through the vengeful mechanoids.
Meanwhile, Megatron and Soundwave had taken control of Cobra headquarters and used the stolen satellite technology to begin producing energon cubes. The Autobots and Joes took the command centre and incapacitated Megatron, but were then alerted to an American nuclear missile headed straight for them. Enlisting the help of Mindbender, the Joes managed to shoot the nuke down with the SPS, with the side-effect of the satellite showering the island with deadly heat-blasts. After the blasts incapacitated most of the Decepticons, Optimus Prime managed to shoot down the satellite and defeat Megatron. Destro, Mindbender, and the Baroness escaped, and Cobra Commander fled with the aid of Starscream.
G.I. Joe vs. the Transformers II
Over the next two years, Cobra rebuilt itself. G.I. Joe continued to bedevil them, breaking up a weapons-smuggling ring and capturing the cyborgified Dreadnoks. Eventually, Cobra hatched a plan to gain access to Teletran 3, a computer that would give Cobra access to Cybertron's space bridge network, allowing for instantaneous troop and supply movements. G.I. Joe agent Chuckles discovered the plan, and led the team to Cobra's Boston headquarters. As the Joes attacked, they disrupted the gate, first sending the Joes, Cobras, and Starscream to Cybertron, and then scattering a number of Transformers throughout time. The time disruption threatened to destroy Earth, forcing Cobra to team up with G.I. Joe to retrieve the missing mechanoids.
Zartan, Storm Shadow, Lady Jaye, and Snake-Eyes were successful in retrieving Jazz, Bumblebee, Hot Rod, and Blitzwing from the 1970s, and the Baroness, Percy, Roadblock, and Beach-Head barely managed to retrieve Optimus Prime and the Stunticons from 1930s Chicago. Meanwhile, Tomax, Xamot, Mindbender, Barbecue, and Spirit found themselves in a nightmarish Decepticon-ruled future Earth. They were forced to take Ratchet back to the present against his will, and both he and Xamot were slain by Shockwave as soon as they returned to Cybertron. The Autobots were taken captive by Shockwave's Decepticons, the time gate was deactivated, and the Joes and Cobras were forced to flee. All seemed lost until Lady Jaye and Roadblock infiltrated the control center and reactivated the time gate, bringing Dusty, Shipwreck, Gung Ho, and a Viper back - along with the fearsome Dinobots. The Dinobots routed Shockwave's forces, giving Joes and Cobras a safe passage home.
G.I. Joe vs. the Transformers: The Art of War
While attacking Area 52 with the monstrous Cobratron, Cobra Commander infiltrated the base and activated the deadly Serpent O.R. in the hopes of controlling the powerful humanoid, only to have him escape to Cybertron and reunite the shattered Decepticon forces. Cobra Commander managed to briefly take mental control of Serpent O.R., but was rendered catatonic when he was exposed to the energies of the Matrix of Leadership.
G.I. Joe vs. the Transformers: Black Horizon
By the arrival of Unicron, a number of Cobra operatives had been captured by G.I. Joe, including Darklon, Overlord, Tomax. The Baroness, Destro, Dr. Mindbender, Firefly, Iron Klaw, and Zartan remained at large.