* BrokenBase: Some people found it to be a great reinvention of the ''Franchise/GIJoe'' franchise, some hated it for the liberities it took and/or more or less basically being ''Series/TheATeam: The Animated Series''.
* CargoShip: ''Shipwrecked'' provides plenty of fuel for both Roadblock x Coyote, and Shipwreck x ''Courtney'' (''Courtney'' being his beat-up old boat).
* CompleteMonster:
** [[VillainWithGoodPublicity Adam [=DeCobray=]/ Cobra Commander]] is the CEO of Cobra Industries, a business organization he uses to cover up COBRA, a ruthless terrorist group. Using COBRA to manufacture everything from weapons to plagues, The Commander [[FrameUp frames a group of soldiers]] who try to reveal Cobra Industries' true colors, sending them on the run for the rest of the series. When the soldiers, called "Joes," continuously meddle in his plans, The Commander has the leader, Duke's, parents kidnapped, offers a deal for their lives, then plans on killing them along with the Joes after the deal is through. The Commander takes no slight against him lightly, shown when he tries to bomb a college to kill one blogger who slanders Cobra Industries, feeds a possible whistleblower to his pet, Serpentor, and [[AndIMustScream seals a metal mask onto James [=McCullen=]]] for leaking information about COBRA. Along with regularly attempting to starve, annihilate, and blackmail entire cities, The Commander has a lethal virus developed that he plans on spreading across the world, then selling the cure only to those who can afford it. After his plan to mind-control the entire planet fails, The Commander plans to use the [[TeleportersAndTransporters M.A.S.S. device]] to transport his armies across the globe and TakeOverTheWorld. When The Joes interfere once again, he [[VillainousBreakdown flies into a rage]], [[NoHoldsBarredBeatdown brutally beats them down]], then tries to [[TakingYouWithMe drag Duke down with him]] when he falls over an edge. Cold-blooded and power-hungry beyond salvation, Cobra Commander once again proves himself to be [[NotSoHarmlessVillain far worse]] than his [[WesternAnimation/GIJoeARealAmericanHero original counterpart]] ever hoped to be.

** [[MadScientist Dr. Mindbender]] is the [[YoungerAndHipper young]], sociopathic, top scientist of COBRA. Commisioned by Cobra Commander to build an army of Bio-Vipers, Mindbender happily tries to feed the Joes to them, and when one of his Vipers escapes and begins causing chaos, Mindbender goes to extra lengths to put civilians in danger. When the people of a town COBRA is plunging into a drought by building a dam begin fighting back against COBRA, Mindbender, along with [[TheDragon The Baroness]], pay [[PsychoForHire Firefly]] to destroy the town and its inhabitants. Tracking down twin psychics, whom he located by torturing a fake medium, Mindbender captures and subjects the twins to horrific experiments. Later, The Joes accidentally release the powerful Electro-Viper onboard a ship, and Mindbender remotely targets it towards [[EvilVsEvil Destro's castle]], completely aware of the destruction the creature would cause once it reaches land. After another of his Vipers escapes, Mindbender [[WouldHurtAChild tortures a young boy]] for the Viper's whereabouts, and later tries to level Brooklyn, New York to act as a distraction while he flees The Joes. Helping build the M.A.S.S. device for COBRA, Mindbender nonchalantly tests it on COBRA's own soldiers, many of whom don't survive, and later tries to send Snake-Eyes through the machine in order to force his best friend to reveal the machine's secrets to Mindbender, then tries to kill them both once the device starts working. Doing everything for [[ForTheEvulz sick thrills]], Mindbender may not have been as powerful or influential as his cohorts, but he far surpassed them in sheer monstrosity
* CrazyAwesome: This incarnation of Snake Eyes. He seems to run on RuleOfCool and UnspokenPlanGuarantee (which is easy since he can't speak). As Duke puts it during one of his many rescues, "What is your crazy friend doing?"
* EvilIsSexy: TheBaroness, as usual.
* MoralEventHorizon: Cobra Commander orders a bomb to destroy an entire college just to murder one blogger who is trying to expose COBRA.
* NightmareFuel: In episode 2, the Bio-Viper absorbs the life out of goats, and you can see their barely alive husks.
** [[spoiler: Possibly Destro's masking, [[NightmareFuel if you imagine those screws being inserted are boring into his skull]]]].
* RescuedFromTheScrappyHeap: Sorta. In past incarnations, Bludd has been, mainly, a mercenary with a British accent and a bloodthirsty streak. In this version, he still is, but he sucks up punishment from the entire team and [[TheDeterminator keeps going]].
* SpiritualLicensee: This show is basically [[Series/TheATeam The A-Team]]: The Animated Series, which most purist fans of ''GIJoe'' feel is an insult to the franchise.
* {{Squick}}: Cobra Commander's pet regurgitating James [=McCullen=]; Scrap-Iron's face after "Rage."
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