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IDW Publishing's original G.I. Joe universe has been the subject of several relaunches, often running as many as three simultaneous ongoing series. To aid the new reader, this article gives a reading order which, whilst not objectively "correct" by any means, attempts to present these stories so as to aid understanding and story flow.

First era (2008–2011)[edit]

  • G.I. Joe #0 (story B), Origins #1–5, #8–10
These two runs of issues comprise Larry Hama's early work on the Origins series, following two of G.I. Joe's earliest missions, and their acquisition of the Pit.
  • Origins #6, #11, #13–15, #19
These further Origins issues are entirely standalone spotlight issues for assorted Joes, with no connection to the wider story. As such, they can be read together here, or instead at essentially any point of the reader's choosing.
The debut arc of the main series, this story begins an ongoing story following G.I. Joe's first encounters with Cobra.
  • Origins #7
This one-shot Mainframe story ties into the main series' second arc, flashing back to several years ago.
  • G.I. Joe #7–12
The second arc of the main series, in which G.I. Joe begin to understand more about their new enemy.
  • G.I. Joe #0 (story C), Cobra #1–4, Special #1
Chuckles infiltrates Cobra, leading to a climax which presumably falls in the aftermath of the main series' second arc.
  • G.I. Joe #13–16
The main series' third arc, which concludes with a three-month gap in-universe, seemingly intended to account for the various tie-in stories.
A one-shot story introducing Helix, who will become a key player in the second half of the main series.
  • Origins #12
A standalone one-shot starring the Baroness, placed here to avoid preceding her introduction as a character.
Chuckles returns in a second mini-series, which a second Cobra: Special follows up on.
  • Origins #16–18
A special three-part story which flashes back to the beginning of the main series.
A mini-series of character spotlights, some of whom have been or will be introduced in the other series.
  • Cobra #5–9
Cobra II is renamed to become a Cobra ongoing series, beginning with an arc featuring Scoop investigating the Coil.
  • Origins #20–23
A four-part story introducing new character the Mad Monk.
The G.I. Joe portion of IDW's Infestation event, in which BATs run amok in an underwater base.
  • G.I. Joe #17–22
The fourth arc of the main series, which sees hostilities between G.I. Joe and Cobra further escalate.
  • G.I. Joe #17–22 & Cobra #10–13
The final arcs of both the main series and Cobra. The Cobra arc occurs after all but the last two pages of the main series, but said pages spoil a major plot development. We consequently leave it to the reader to read this issues in an order that suits them.

Second era (2011–2013)[edit]

The one-shot introductory issue that begins the "Cobra Civil War" event.
In the opening battles of the Cobra Civil War, the Pit comes under attack, Snake Eyes leads a team to the Himilayas, and the Joes have a mole in their midst.
  • G.I. Joe vol. 2 #5–8
  • Snake Eyes #5–8
  • Cobra vol. 2 #5–8
In the second set of Cobra Civil War stories, a Joe team find themselves trapped in Springfield, Snake Eyes fights to stop a powerful virus, and a race begins to root out the traitor.
The second Infestation story, which sees a Cobra researcher summon an unspeakable terror from beyond.
With the new Cobra Commander appointed, this Annual flashes back in time to tell their life story.
This story sees Cobra attack Nanzhao in a crossover encompassing all three books. See the "Cobra Command" article for the issue order.
  • G.I. Joe vol. 2 #12
  • Snake Eyes #12
  • Cobra vol. 2 #12
These three issues comprise "Cobra Command: Aftermath", each examining the fallout from the crossover.
  • G.I. Joe vol. 2 #13–16
  • Snake Eyes and Storm Shadow #13–16
  • Cobra vol. 2 #13–16
In the third arcs of the books, the Joes become trapped deep underground, Snake Eyes joins with Storm Shadow's ninja clan, and Flint assumes command of the intelligence division.
  • G.I. Joe vol. 2 #17
  • Snake Eyes and Storm Shadow #17
G.I. Joe and Snake Eyes pave the way for the "Target: Snake Eyes" crossover story in these two issues.
This story crosses over G.I. Joe and Snake Eyes as both the Joes and Cobra hunt the enigmatic ninja. See the "Target: Snake Eyes" article for the issue order.
  • G.I. Joe vol. 2 #21
  • Snake Eyes and Storm Shadow #21
In the aftermath of "Target: Snake Eyes", G.I. Joe and Snake Eyes come to a close.
  • Cobra vol. 2 #17–21
In Cobra's fourth arc, the G.I. Joe intelligence division must contend with the Oktober Guard.

Third era (2013–2014)[edit]

Fourth era (2014–2015)[edit]