Starting in April of 2011, IDW created an overall story line called Cobra Civil War that encompasses three individual GI Joe comic series. This story line is about the Cobra organization's attempt to fill the position of Cobra Commander after the previous holder of the position was killed by Chuckles. The position of Cobra Commander is elected and the campaign to win the election is based off which Cobra can kill the most GI Joes.
This series directly follows the previous GI Joe: Cobra title and is tied into the current events surrounding the Cobra Civil War. Basically, this is the internal view of Cobra as it fights its own Civil War.
Cobra: Cobra Civil War is written by Mike Costa.
The first issue #0 is a combined issue that tells a 10 page story from all three series. Issue #1 was released in May of 2011.
The 100 page Cobra Commander Tribute issue also contains brief comments regarding the Commander's death. Cobra Commander Tribute.
Released in January of 2012, the first Cobra Annual: The Origin of Cobra Commander tells the entire history of the character that becomes the new Cobra Commander for Cobra after the Civil War storyline is concluded. The new Cobra Commander is revealed in issue #8 of GI Joe: Cobra Civil War.
Starting in January 2012 with issue #9 after the new Cobra Commander takes over the subtitle changes from Cobra Civil War to Cobra Command. The Cobra Command storyline is literally one storyline played through all three series. The Cobra title is always the third part of story for each month parts being 3,6 & 9 of the story.
The additional series that support this story line are GI Joe: Cobra Civil War/Cobra Command and Snake Eyes: Cobra Civil War/Cobra Command.