Yeah, but my summary will kind of suck. Still, possible SPOILERS AHEAD...
It starts out in flashback with one of Destro's ancestors being tried for insurrection or something for providing arms to Louis XIV, and his punishment is that he has an iron mask sealed to his face. Flash forward to the present, and current Destro/McCullen/whatever is presenting something to the UN about nanobites or some super bug tech weapon. Hawk is there and hears about it. IIRC, he and Destro are kind of working together to get some warheads shipped somewhere, but Hawk is suspicious of him.
Duke and Ripcord--who apparently aren't Joes yet--are doing something to facilitate safe transfer of the warheads when the Baroness, Storm Shadow and a bunch of Nano Vipers try and intercept the warheads. Ripcord is apparently a bumbling, goofy, Jar Jar Binks type character who keeps screwing up in all the right ways. Naturally, after the battle, he and Duke are recruited to join G.I. Joe. Hawk somehow winds up in a wheelchair, and there is some kind of cool Cobra Typhoon airship or something.
Then there's a flashback about how Duke used to date the Baroness (Ana DeCobray) but she dumped him after he accidentally got her brother killed. As it turns out, however, her brother isn't really dead, but is working for Destro as The Doctor (not Mindbender...you'll see why in a second). Plus Baroness isn't really evil, but she's under some kind of mind control, and Duke knows this, but it doesn't stop him from wanting to kill her. Also at some point, Snake Eyes' backstory is retconned to make him a French orphan who is taken in by the Arishikage clan and the Snake Eyes/Storm Shadow sword brother story is told.
Eventually, it is discovered that Destro's up to no good and has been in cahoots with the Baroness trying to double deal on the warheads. Destro releases his nanotech weapon on the Eiffel Tower, and the Joes try to save the day using some kind of kick ass super body armor. They fail, and the Eiffel Tower goes down. Then Hawk sends the Joes (via Submarine, piloted by Shipwreck) to attack Destro's underwater arctic base. During the battle, The Doctor gets some kind of nanogoo on his face, and gets pissed and starts calling himself The Commander (dun-dun-dun). Then the Joes save the day, but Cobra Commander vows revenge.
Wow. It sounds even worse when I tell it.