- When Mike goes on a violent spree with SIE as his handler in Marburg's mansion, she'll orgiastically start humming "The Ride of the Valkyries".
- "Oh, great. It's a picture of Darcy. It says 'Mike and Sean, fuck yeah!!!' with three exclamation points."
- "Two words: horse porn. All over your computer."
- "I wonder how many gay cheetahs had to die to make that jacket?"
- One of Heck's greatest lines ever:
"Oh, yeah, I name all the operations that go down in Taipei. Even the ones that aren't mine! Operation Latex Turtle, Operation Angry Bees, Operation AAAAAAAAHHH-YOOOOOOOOOW! Heh. That was a good one."
- Some of Michael's email replies to Heck are hysterical. During one of Heck's longwinded Conspiracy Kitchen Sink emails, one response Michael can give is:
"Dear Steven, Please shut the fuck up. Sincerely, Michael Thorton."
- You can also reply by quoting Time Cube at him. Gives double positive influence, too.
- The NSA listening post in Rome. Mike's facial expressions in this scene are pure comedy gold. You'll know it when you see it.
- One of Mike's possible responses when Deng orders him to get into a maintenance closet at gunpoint:
"This is going to end with me pointing out where you touched me on the doll, isn't it?"
- If Mike is a veteran, while traveling through the catacombs of the ruins in Rome he'll start to hum something called "Sinister Music" by the subtitles. Mike actually sings the tune in time with the flickering lights.
- If Mike agrees to let SIE...release him...and is agreeing to destroy Alpha Protocol, Westridge has some hilarious things to say about it afterwards.
Westridge: You did not just do that in my medical bay. Bet it smells like cat piss and tuna in there...
- Mike getting fed up with Grigori and beating the crap out of him. It starts off as a bit shocking, but then turns darkly humorous from Mike's commentary.
Mike: (after smashing a bottle over Grigori's head) Aww, you spilled your wodka.
- Mina's "Advanced Shooting Range": sneaking up on Darcy and tranqing him in the melon. While he scoffs about how easy the shooting range is.
Darcy: (from the floor, slurring and muffled) Lucky shot!
- It's even better when you shoot him in the balls. Mina is especially pleased.
- By choosing to accept Mina's "challenge," you will then hear Darcy badmouthing Mike's performance on the course.
Mike: Give me the gun.
- Sparing Brayko results one of the funniest news broadcasts in the game:
INN Newscaster: Authorities say that he will be charged as soon as he is well enough to be discharged. Mr. Brayko had no statememt for the press, but while he was being loaded into the ambulance, he was heard to remark that the party responsible for the attack "an expletive American commando cowboy like the expletive offspring of Ronald Reagan and an expletive American Ninja." ... a source within the hospital stated, that, quote, "The man had enough cocaine in him to make a baleen whale see Jesus."
- If you have Heck as your Handler during the endgame, you got this conversation when your chopper gets blown up.
Heck: I got good news and bad news, the bad news is that was our ride out of here.
Mike: And the good news?
Heck: I paid extra on the insurance package.
- If you agree to let Albatross be your handler for the mission at the US Embassy in Moscow, and choose the Suave response:
Mike: Alright, I'll bring the marshmallows, you bring the hotdogs.
Albatross: This is no time to joke.
Mike: If you're too cheap to bring the hotdogs, just say so. Guess those G22 resources aren't all they're cracked up to be.
- Aggressive!Mike is an endless font of misanthropic hilarity.
Mina: Now that you've made it to Taipei, what are your plans?
Mike: Mostly I figured I'd punch somebody until answers came out.
Madison: Ever hear of 'anger management'?
Mike: No, because I killed all my therapists.
- Mina and SIE's sniping at each other. These two women really don't like each other.
- Heck saves the day.
- In the endgame, with the inimitable Steven Heck: 'Should I file that under M, for Mangled in Woodchipper, or W, for Woodchipper, Mangled?'
- Brayko to Surkov: "Your bodyguard is winning gold medal in dying. I gave him 6.4 on the dismount but he did not stick the landing."