The Joes are called in by the US President to recover some nukes in Pakistan. They do. Just as they are waited to be extracted, it is revealed that the president is being impersonated by a Cobra guy. They get attacked and only 3 survive. They blame everything on the Joes. They make their way back to the US and set up in an rec centre after calling in some favours.
We see Snake Eyes getting put into the weird prison Cobra Commander and Destro are in. It is revealed the Snake Eyes is really the Cobra Ninja in disguise. He then does ninja stuff and frees Cobra Commander and for whatever reason they leave Destro.
The Joes contact the real Snake Eyes, he's at his ninja lair with a new ninja, Jinx. She's the Cobra ninja's sister or something. They go after the Cobra Ninja and catch him. They make up as it turns out Cobra has backstabbed the Cobra Ninja. They team up and head to the US and all meet up in the rec centre. They go see Bruce Willis, who is the original Joe. They make a plan to attack the fake president and free the real one.
The fake president calls a meeting with all the world leaders that have nukes to disarm. They don't agree, so the Fake Pres shoots all his nukes and the other countries follow suit. He then destroys all his nukes as they are in the air the other countries again follow suit. The world is in full nuclear disarmament, but the fake pres has a bunch of satellites that shoot nukes and he shoots London. They are waiting for the other satellites to line up. The Joes attack and stop the other satellites, blowing them up. They free the real president and all get medals. The End.