These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Best Level Ever: The assault on Brayko's mansion is amazing, at least for a Mike built for combat. Gunning down a small army of tracksuited mooks while hard rock blares in the background is an absolute thrill.
Big Lipped Alligator Moment: In a Veteran playthrough, when Mike first speaks to Mina via PDA, the image of her face is briefly replaced by the gelato man.
Complete Monster: Halbech's CEO Henry Leland is a Corrupt Corporate Executive who knows absolutely no boundaries in his goal to make profit out of the suffering from others. Throughout the game it is revealed piece by piece that he is behind pretty much every major crime in the story. Among many other things, he provided the resources and the objective for the terroristic cell Al-Samad to shoot down a civilian airliner, he had Mike join Alpha Protocol with the intent of killing him when he stopped being useful, he ordered the assassination of Taiwan's president and he sent Conrad Marburg to assault the heavily visited Museum of Arts in Rome, where Mike is forced to choose between a friend (or loved one, depending on the choices) and a whole room of civilians. His overall goal is to destabilize the world and drive humanity to the brink of World War 3, just so he can make a fortune out of it. His preferred method of recruiting underlings is ruining their lives and thus practically forcing them into his services, as he did with Marburg and also tries with Mike. If the player accepts this, he shows that once he has no more use for his people, he throws them away like dirt, by ordering Mike to execute anyone who knew of his plans, including Mina. Coldly calculating, merciless and with a smug and false friendliness to add insult to injury, Leland truly earns his role as the biggest bastard throughout the game.
Steven Heck; he invented his own form of insanity-based martial arts, he's an incoherent conspiracy theorist, and if you quote Timecube lore to him he thinks you're serious. And then there's the subway minigun drive-by. It even says in his complete dossier that either he is the greatest CIA spook of all time, or he's a random guy who has turned into one of the best spies in the world through sheer power of crazy. But then there's that CIA mail about a 'rogue' seen in Taipei, and it's clear it's not about you. That leaves only one guy...
Really, Leland? A yellow tie and yellow shirt with your business suit? Mike can even lampshade it (although not to his face, unfortunately).
Brayko and his 'gay cheetah' jacket. In one dialog option, Mike says it wasn't difficult creeping around Brayko's mansion because that jacket of his was so loud it distracted the guards. He doesn't even mind.
During the Rome final mission, to save Madison, you have to go to the West Wing (left). To disarm the bombs, you have to go to the East Wing (right). In other words, saving Madison is the Suave decision, going after the bombs is the Professional decision.
While Brayko's line referring to Thorton as the "(expletive) offspring of Ronald Reagan and the (expletive) American Ninja" is always funny, it makes more sense that he'd say something like that when you remember that he is after all, a fan of American 80's pop-culture.
Scarlet Lake, intrepid photojournalist. Willing to run as many stories exposing major Halbech scandals as you can email to her. But given that you are personally acquainted with just how extreme Halbech's overkill can get when trying to hush up one scandal, how on Earth is she living long enough to publish all of them? Well, it probably helps that journalist is only her day job, and her night job is "master assassin." Also in that Halbech needs her to live long enough to at least finish the Taipei assassination they hired her for.
In Taipei, who's the one who sent you the faulty information about who's trying to assassinate Sung? The Triads. But where are they getting THEIR information from? Steven Heck. Note that Leland knows about Steven Heck even though Heck is not listed as an agent on any payroll. It's entirely likely that Heck was hired by Halbech to sow misinformation during the Taipei mission to let the real assassin run free. There's even been a Shrug of God about this.
Heck even says that he thought Michael knew Scarlet was the assassin, and just wanted to boink her in spite of it. "I thought it was pretty classy of you." Hehe.
Upgraded flashbangs, especially against bosses. It's possible to take down Brayko in one long barrage of fire if you catch him with a flashbang before he snorts another round of his hyper-knife-killy cocaine. Also maxed out Chain Shot can bring down a boss' HP bar from max to almost zero.
Chain Shot is practically an "I Win" button; the basic version will just take out a couple of guys, letting you make kills easily and without being seen or thinning the crowd in a tense firefight. At higher levels, where you get up to six shots and plenty of time to mark them, Chain Shot will clear the room more efficiently and accurately than a rifle or shotgun. Combine with Brilliance, which resets your cooldown timers, and it goes from "bring a boss' HP to almost zero" to "the boss is dead before he fires his first shot."
Incendiary grenades are boss breakers. Watch as their auto-regen health tricks DON'T WORK! See them cower as all their life is taken away while you stand behind cover twiddling your thumbs! Observe their now total lack of armor!
Just about any of the skills can be this if they get maxed out. Maximum Toughness Mike loaded with the heaviest armor can take hits that would literally destroy tanks and not even slow down - and that's before triggering Iron Will. Maxed-out Martial Arts lets Mike take apart bosses in hand-to-hand without any sweat, up to and including cocaine-boosted Brayko. Maxed-out Stealth allows Mike to trigger Shadow Operative and sprint around for twenty seconds while invisible and allows him to one-shot guards. Even the Sabotage and Technical Aptitude sets offer some rather impressive benefits, ranging from boosting the effectiveness of gadgets to allowing Mike to dramatically improve his weapons, armor, and med kits.
Not necessary maxed out, even. Level 13 Martial Arts Skill, the Point Blank Shot, while moderately useful in combating Mooks, can be used to end boss fight within seconds, provided that you can get in range for HTH. Against Omen Deng and Marburg it's certified perfect. The trick is, the shot is treated like end of the combo, so it lets you chain several combos together.
Higher levels of Stealth make walking through the game simplicity in itself. At maximum level, Thorton can basically turn invisible, wade into groups of Mooks, one-shot them all with martial arts takedowns when they're mere inches from one another, and swiftly retreat for a ludicrously quick cooldown period before doing it all over again.
Mike: Hey, Darcy photoshopped our faces into a still-frame from a buddy-cop movie. That's... yeah.
Also Mike and Heck.
Love It or Hate It: "Divisive" doesn't even begin to describe the game's reception. To some, Alpha Protocol represents the gold standard of gaming narrative and design, with depth and complexity to rival Mass Effect and Deus Ex. To others, it is a frustrating, disorganized, nigh-unplayable shambles that never should have been released.
Thorton, arguably. In one ending he sticks Westridge and Leland with the blame for the stolen missiles, which it was. By threatening Parker with the fact that once what Halbech and Alpha Protocol becomes public Parker will be stuck holding the bag he convinces Parker to help him preserve the evidence of Alpha Protocol's involvement. Naturally, Leland protests that he has powerful friends who will protect him, to which Thorton replies that they can'tsince it would require admitting that not only does Alpha Protocol exist but that it is sanctioned by the US government.
Combine with Manipulative Bastard when you consider that Mike allowed Madison to die because he'd just found out that she is Alan Parker's daughter - note in the dossier that it specifically tells the player just how Parker would react if something bad happened to her. It's specifically urging the player to make sure Madison dies just so Mike has ammunition against Parker.
Memetic Bad Ass: There's one or two theories on the official forum that the true architect of AP's plot is none other than... the Gelato Man.
Paranoia Fuel: Mike can purchase mapping information from an online company called SecuritySift that provides complete layouts of mission areas. It starts to get worrying when it becomes apparent that these guys have maps of everything - they even know where automated machine gun turrets, security locks, and guard patrols are. And their prices are surprisingly cheap, implying that they're not sending agents out to actually scout, but simply have this information on hand. Just how much data does SecuritySift actually have?
Player Punch: Marburg forces Mike to choose between stopping a bomb and saving Madison. Right after the player might sleep with her. It's made even worse because, if you don't do the right things, you might not even get the opportunity for revenge.
Scrappy Mechanic: The hacking minigame, at least on a PC. Described by one GameFAQs poster as "A word hunt on heroin", it features confusing & unmappable controls, a headache-inducing interface, a very tight time limit and best of all triggers an alarm if you screw up. Threads abound across game forums complaining about this one, horrible minigame. The minigame to disable alarms (which you probably set off hacking) is an eyestrainer too, but at least can generally be completed within normal human reaction times.
The boss fight near the end against Darcy, because he keeps pelting you with grenades at ground level from a guard tower, making him difficult to hit. Ugh.
This one can be made easier if you have at least one EMP charge, however, because you can hack the door to the tower opposite Darcy's, and pick up the sniper rifle at the top to take Darcy out with a headshot.
And of course, poor Wen... so much abuse laden upon the poor guy by Heck. Then again, Wen might deserve it. Heck did mention that Wen was NOT a stand up guy. Which may translate into: Tried to kill/sell me out.