A new series by IDW publishing based on the eponymous franchise. The comic book series is a complete reboot of the franchise with its own sense of continuity. The series began in 2008 with ''G.I. Joe'', which began a new series of adventures revolving around uncovering a mysterious and hitherto-unknown organization known only as Cobra, and ''G.I. Joe: Origins'', which explored the origins and personalities of various characters, including Duke, Snake-Eyes, Scarlett, and others.
There was also a mini-series called ''G.I. Joe: Cobra'', which revolves around Chuckles, the Joes' undercover agent, as he infiltrates Cobra. His story continued in ''G.I. Joe: Cobra II'', culminating in Chuckles, through his own efforts, as well as being a pawn in the schemes of the various factions within Cobra, assassinating the Cobra Commander in a major plot-twist.
After that, the story took in the ''G.I. Joe: Cobra Civil'' War a major turn as the various leaders of Cobra, which up till then focused on maintaining a low profile, tried to prove themselves worthy of the mantle of Cobra Commander by striking against G.I. Joe and against each other. These various attacks cause major damage to the Joes and cause political pressure to force them to downsize. A new character called Krake won the prize, and the story ended with the appointment with a new Cobra Commander. A new series called ''G.I. Joe: Cobra Command'' was published detailing the reign of this new Commander. Whereas the previous Commander insisted on secrecy and stealth, focused on subversion and behind-the-scenes manipulation and secret technological development, and was willing to tolerate some independence among his subordinates, the new Commander is far more militaristic, controlling and openly aggressive. He launches Cobra into the limelight first by using Cobra's massive arsenal to conquer and effectively destroy an entire nation, and then by exposing G.I. Joe to the world.
The story is still on-going.
* BadAss: Oh, yes. There are many notable bad asses on both G.I. Joe and Cobra. Particularly noteworthy badasses are Snake Eyes, Storm Shadow, and Helix.
* BodybagTrick: Kwinn and Lighthorse smuggle Snake-Eyes across the border by hiding him in a coffin in a hearse.
* CodeName: Naturally. The Joe's are officially listed as KIA, and their codenames are considered their REAL names.
* DarkerAndEdgier: Compared to the cartoon, hoo boy. All members of G.I. Joe, with the exception of General Hawk, are listed as KIA and are all officially dead. The Joes regularly use lethal force when necessary. Cobra soldiers are shown to be quite capable of killing the Joes in return. Cobra is shown to be an effective organization that regularly uses torture, psychological manipulation, death, and even weapons of mass destruction when doing so will further their goals. Characters on both sides die. All of this is justified since the Joes are highly trained black-ops soldiers, and Cobra is a terrorist organization. Issue #6 retconned Cover Girl's backstory; she is now said to have given up being a model because she would much rather do something she was good at - kill people. Not a motivation you would have ever seen in the original cartoon series or early comic books in a character who is not a member of Cobra.
* DarkAndTroubledPast: Several of the characters have troubled pasts, many of which are revealed in G.I. Joe: Origins. Of note is Krake, the New Cobra Commander, who was born and raised in the opium fields of the (fictional) country of Nanzhao, where there is perpetual war among the drug warlords.
* DirtyHarriet: In ''G.I. Joe: Cobra'', Jinx poses as a stripper in a strip club in order to make contact with Chuckles.
* DroppedABridgeOnHim: This was done to the entirety of the Ninja Force (generally considered an embarrassment from the DorkAge of the toy line and the unfortunate final days of ''ComicBook/GIJoeARealAmericanHeroMarvel''); having them brutally murdered during the 'Cobra Civil War' arc as part of a competition by contenders for the Cobra Commander position to see who could kill the most Joes.
* TheFaceless: Both Cobra Commanders, naturally. Snake Eyes as well.
* FromBadToWorse: After the death of the first Commander at the hands of the GI Joe secret agent Chuckles, Cobra goes nuts, forgoing its obsession for secrecy. the Council that governs and funds Cobra states that whoever kills the most Joes becomes the next Cobra. The Joes lose two major military bases, their submarine, and countless teammates. This causes them to suffer drastic budget cuts. THEN, Krake becomes Cobra Commander, and within two weeks he proceeds to wipe out a country, destroying it's countryside, evicting or killing it's citizens and nuking it's cities.
* FromNobodyToNightmare: Krake. A poor rural boy from the country of Nanzhao (apparently the stand-in for Burma/Myanmar) who rises to become a member of the High Command of Cobra, to the Commander himself. Monk is shaping up to be this for Duke specifically; from ordinary(if trigger-happy) U.S. soldier to brutally sadistic head of Cobra's New York division, and oh yeah, he's spent years messing with bank records to make it look like Duke's on the take.
* GenderFlip: A few of the Joes have been reimagined as women instead of men, most notably Dial-Tone and Doc.
* GoodIsNotNice: G.I. Joe is a team of soldiers, not superheroes. The Joes have no problem killing their enemies or any threat to their person.
* GroinAttack: In ''G.I. Joe'' #6, Cover Girl takes down a pirate by shooting him the groin with a paintball gun. (At least, we ''think'' it's a paintball gun, considering she quickly offs everyone else rather brutally.)
* HighlyVisibleNinja: Much like in the original series, Storm Shadow still constantly wears white. The Arashikage clan ninjas are sometimes worse. For example, when they are operating in a jungle environment, they wear RED clothes.
* ItGetsEasier: Strongly implied with Cover Girl's ease at slaughtering people in issue #6.
* NiceJobBreakingItHero: Deep-cover operative Chuckles and his handler Jinx try and infiltrate Cobra. Jinx is discovered and Chuckles has to kill her(after falling in love with her) to prove his loyalty to Cobra. Eventually Xamot reveals that he knew Chuckles was a Joe all along, and basically forced him to kill her [[ForTheLulz just for the hell of it.]] Chuckles, however, eventually impresses Cobra Commander enough that CC hands him a loaded rifle and gives him permission to shoot Xamot. Chuckles mutters "Yo Joe", then swings around and kills Cobra Commander, then finishes off his mission by detonating a Cobra warhead and destroying the base, costing them hundreds of millions of dollars in materiel and personnel. While this does put Cobra into flux for a while, it's a ''bad'' sort of flux, where all the top rank are battling for control, and when one of them eventually becomes the new Cobra Commander, he's ''much'' less concerned with Cobra's public image and begins to take the fight to G.I. Joe in a big way.
* NotADate: At the end of ''G.I. Joe'' #5, Doc and Quick Kick use their leave time to see a Broadway show. They quickly and forcefully tell Duke and Cover Girl that it's "Not a date!", despite neither Duke or Cover Girl suggesting that it was.
* NotWithTheSafetyOnYouWont: The Baroness pulls this trick on Hashtag in ''G.I. Joe'' #5, telling her that the clip in her pistol is empty. When Hashtag tilts the gun to check, the Baroness attacks and wrests the gun off her.
* PinPullingTeeth: Zartan does this when being pursued by the Dreadnoks in ''Special Missions'' #7; his other hand being occupied in steering his motorbike.
* RuthlessModernPirates: ''G.I. Joe'' #6 tells Cover Girl's origin story, which involves her taking out a gang of ruthless modern pirates while a contestant on a celebrity reality show.