The climax, when Duke traps Cobra Commander in his own safe room, then targets the Kill Sat on Cobra's headquarters in Springfield, blowing up the entire facility just as Duke and the others make their escape.
Snake Eyes, every moment he's on the screen. From his complete annihilation of the COBRA Troopers on the Arashikage Island, to his showdown with Storm Shadow, to his Dynamic Entry at the end, he is a walking, hacking, slashing, shooting, killing-with-a-mere-flick-of-the-wrist CMOA.
From the villains' side of things, the new and improved Cobra Commander, who's jumped from a comically ineffectual villain to a psychotic tyrant who;s willing to cut down anyone in his path to achieve his goals, and within the first few minutes of the show, delivers an ultimatum to the U.N. via a Kill Sat that sears Moscow off the face of the planet in a matter of moments. Not to mention afterwords, he completely shuts down any possible attempts at betrayal from his subordinates with this speech. Charlie Adler's delivery just sells it.
Cobra Commander: And this, is how I win the world. This juncture, of course, is usually where the wheels come off, but not this time. Cutting the traitor Major Bludd's heart in half right in front of you, right here in this room, should've gotten the point across. It suited me once to appear weak and cowardly, because it motivated you people to think! But today is a new day. There will be no move to take over my command. There will be no mistakes. There will be none of your CRAP! NONE OF IT! ... Work with me and I will give you the world in less than twenty-four hours. Work against me and I will gut you like a fish. Right here.
Even when things start going wrong, and his plan is falling apart around him, Cobra Commander doesn't whine. He doesn't try to run. Instead, it's revealed that not only was he Crazy-Prepared enough to have a secondKill SatWave Motion Gun ready in case the main one was taken offline, and nearly wipes out the Joes with it. After that, it's all one frightening Villainous Breakdown that makes Cobra Commander seem even more dangerous:
Cobra Commander: Less than twelve hours, and it's all. Gone. Wrong. I mean, you know I missed some of [the Joes] with the cannon shot! (Voice drops a venomous octave) You know it.
(Troops share a worried glance)
COBRA Commander:There is only one thing to do. Ramp up the reactor output! I want to start striking cities randomly, until they give me what I WANT!!
When one of his own soldiers points out that it's going to take a couple hours to charge up the Kill Sat for that kind of mass destruction, Cobra Commander executes the hapless trooper with his saber, then coldly tells the rest of the staff to dispose of the corpse.
When the Joes show up, he directs his forces to engage them rather than run away.
By the time Duke gets to the control room, Cobra Commander has slaughtered his staff for reasons known only to his own twisted mind, using their blood to paint a Cobra insignia on an observation window.
Taunting Duke from within a heavily-armored shield chamber, informing him that when the Kill Sat fires, it's going to wipe out Washington D.C.
When Duke re-aligns the targeting coordinates so that the Kill Sat is targeting Cobra Commander's base, and shoots out the controls for the protective chamber so that CC can't escape, the insane tyrant lets out a scream of rage rather than break down in a sniveling, cowering mess.
All throughout, Cobra Commander's attitude ranges from incensed fury at the way his plan is falling apart, to venomously taunting Duke about his helplessness to stop the Kill Sat from firing, to screaming in incoherent rage as he realizes that Duke's re-set the coordinates so that the ion cannon fires on him, and that he's trapped in his own protective chamber. It's rather quite chilling to watch.