Cobra Commander is mutated into a huge yellow cobra, and in his last act in the story, he attacks the snake Serpentor threw at Lt. Falcon. Actual king cobras are yellow, and they eat other snakes.
Seeing Cobra Commander completely unmasked and knowing what he is makes a scene from one of the early episodes make a lot more sense. Destro walks in on an un-masked Cobra Commander eating. He demands that the Commander put his hood back on; he chuckles and replies "It takes a strong stomach to watch me eat, doesn't it, Destro?"
This could count as Brilliance, Horror, or Funny if you're so inclined: The intro features a prominent shot of Major Bludd getting his C.L.A.W. shot right off his back at around head height to the Statue of Liberty. He's absent for the rest of the movie. Ouch.
Actually subverted. He is seen with the rest of the Cobras getting berated by Serpentor in the next scene.
Destro's ready acceptance of Golobulus's taking the credit for Serpentor's creation makes perfect sense considering his current predicament. He is in the middle of a completely alien civilization and surrounded by an army of strange soldiers and weapons, having just been rescued by them from the Joes. Whatever gets him on their good side is what he will say.
The nature of Cobra-La as a civilization of reptilians bent on world domination suddenly makes the "Lizard Man" conspiracy theory take on a different light.
While Duke's hastily undone demise is due to the reaction to Optimus Prime's demise in the Transformers movie, it's still plausible for him to survive. In human anatomy, the heart is located between the lungs, whereas Duke was hit close to his shoulder. While it's still a serious injury, it's not too far for Duke to survive.
Those Joes who were freed from the "trees" should have still gotten injured, severely for those with helmets, and fatally for those without. Vines wrapped around you are a poor choice for something to break your fall.
The big explosion at the end when the B.E.T. overloads is clearly a nuclear one. That the heroes weren't all reduced to atomic shadows means that they, or most of them, are doomed to a slow painful demise from radiation sickness.
