The Ion Cannon. From the moment you activate it a light rain starts up out of nowhere as the atmosphere ionizes, columns of light swirl together over the target, and... BOOM, everyone dies.
A cutscene begins with a Nod commander ordering the immolation of several civilians. Needless to say this provokes a very pissed off, "REAL TOUGH GUY!?" from the player Commando who promptly snipes said commander in between the eyes.
Of course, this being a game based on the aforementioned Commando, there are tons of lines like that. Paraphrased example:
Prisoner: "You're going up against an entire enemy ship by yourself?"
Havoc: "Doesn't seem fair, does it? Maybe I'll shoot left-handed."
Earlier in the same level, two Nod soldiers are checking out the submarine int he ship's hold.
Nod Soldier 1: "Check it out. It's one of those new subs!"
Nod Soldier 2: "Impressive! Is it armed?"
Havoc: (hops out out of the sub and shoots both of them in an instant with his pistol)"This one is!"
One of the themes is based around Havoc's Catch-Phrase "I got a present for ya".
That catchphrase also formed the startup screen for the N64 port, in which the Commando blows up the N64 logo.
Also said by the equally badass Colonel Burton who can literally take a tank on himself, and beat it just by shooting his rifle at it.