- Cobra Commander is the Cobra leader in the IDW continuity.
The first Cobra Commander seen was a well-known, famous businessman, operating as the Commander in secret. His uniform was a suit and tie, with gloves and variation of the silver face mask. Rather than having an army helmet over the blank face plate mask, the lower portion of the mask around the jaw line has fangs engraved on the mask.
Unlike other incarnations of the character, this version of Cobra Commander - usually just called "the Commander" - is extremely reclusive and his existence is only known to only select high profile Cobra subordinates (such as the Crimson Twins Tomax and Xamot and Baroness). Cobra Commander's personality is also much more passive-aggressive and introspective; having captured the G.I. Joe spy Chuckles, Cobra Commander refused to allow Tomax and Xamot to kill the spy, opting instead to attempt to personally recruit Chuckles by taking him into his confidence and promising him revenge against Xamot.
In issue #12 of "G.I. Joe: Cobra", Xamot attempts to set up Cobra Commander to be killed and Chuckles to be blamed, only to learn the Commander knew about this and has outmanouvred him, giving Chuckles the chance to kill him. Ironically, Chuckles does kill the Commander instead, shooting him through the head. A competition erupted in Cobra to find who will be the replacement, directed by the Cobra Council.
The contest turned out to be who could kill the most Joes: Cobra agents Baroness, Dr. Vargas, Major Bludd, Oda Satori, Tomax, Krake, and Raja Khallikhan were all in the running. Baroness, however, doesn't believe the Council would make her the Commander as she's a woman - not that this stops her killing Joes. In the end, Krake wins the competition, largely by revealing that he had killed and replaced one of his rivals with Zartan, doubling his kill score and showing the initiative to break the rules to win.
- Of all the numerous Cobra Commander incarnations, IDW's incarnation was the first and so far the only incarnation to be killed-off in the G.I. Joe media.
- G.I. Joe: Origins involved a psychotic ex-stock broker who murdered his family and several law enforcement officers when his crimes were discovered. Calling himself "the Chimera" and gathering a militia around him, he was one of the first villains G.I. Joe faced. Larry Hama intended him to be Cobra Commander, but this idea was dropped with the introduction of the Cobra Council and has not been seen since Origins #5, and it's not been specified since if he was indeed the Cobra Commander that Chuckles murdered. (Also of note is that he started the sub-prime mortgage crisis of the late 2000s)