I told Carlos what happens in the movie.
See, Duke and Scar hook up. The Joes are fighting Cobra on US soil and it's a huge war. Joes use the Sigma6-like Mechs and battle away the wave after wave of Cobra planes and flying BATs.
Deciding that only Duke can defeat Destro (he is, afterall, the main problem) so he takes a Thunderwing (w/ Scarlet). On the way there, there's a huge explosion and Duke goes blind. Scarlet has to fly the Thunderwing into the heart of Destro's base. They dodge bullets, plasma rounds, etc. The plane takes a gnarly hit and they go crashing down. Scarlet ends up with a large piece of metal thru her chest and Duke manages to tell her that he loves her before she dies.
Duke makes his way out into the warzone. He's blind and helpless.
Deciding he can't do much more, he activates the nukes that are both on the plane AND on himself.
The nukes destroy the comptuers used to control the flying BATs and air force. They fall to the ground, exploding in a very huge way. Slipstream and Ace are seen walking away from the helicarrier with cigars in their mouths. Their women come running up as well as the president and Ace's dad. Ace picks up his kid and says, "See, daddy told you there'd be fireworks..."
The very last scene has General Hawk sitting on a bench in a ruined New York City. Cobra Commander comes walking up behind and says, "How do we know this will work? Can you people really rebuild the world and let us co-exist? I'll release the world..."
And then the screen turns dark and funky green writing scrolls on the screen...
(yes, I'm taking a break from working on GIS at school)