- It's kind of sweet that thousands of people turn up for Madison's funeral in the streets of Rome if she dies, as you discover in the end credits, albeit politically complicated and used as an excuse to pass an extreme law.
- In an equally bittersweet moment, thousands of people also turn up to hold a candlelight vigil for the hundreds killed in the bombing if Madison lives, with Madison herself leading the crowd, with the implication that Madison is also becoming a political leader that fights against corrupt anti-terror legislation, with her main argument being that the human rights violations used by such laws aren't effective with curbing acts of terror.
- Any positive-outcome conversation with Mina if you romanced her.
- Similarly, the positive-outcome conversations with a romanced Scarlet. Especially in the ending, where she readily admits she was the sniper in Taipei and tries to apologize, only for Mike to forgive her on the spot. (It's more bittersweet in that you almost always have to let Mina die for the outcome.)
- If Sis is the one who comes to free you from the medical bay towards the end of the game, there's the moment when she undoes the restraints and helps an apparently drugged Mike to stand up. And he's a fair bit taller and bigger than she is, so she kinda almost buckles; it's a mirror to the scene where you spare her earlier in the game. Debt repaid.
- The ridiculously sad look Mike gives her when she does so (you can only guess at her backstory, but it's probably not pretty) and her firm expression before calmly walking away makes it kind of depressing, too.
- Though it's really sweet if you have a positive rep with her and she smiles before tossing you a pistol
- Whatever the story is behind Sis's locket, the reason she gives it to you is obvious: surviving the battle with you and giving it to you represents letting go of her childhood.Albatross: She gave you that? ...It's a childhood memento. Perhaps those days are over.
- Or that Sis has a new father figure (or possible Love Interest). Note Albatross gives a negative reaction to finding out she gave Mike the locket.
- Saving Albatross or SIE from Brayko's clutches qualifies.
- Having a Friendship with Albatross during the entire game, generally, is one long Crowning Moment of Heartwarming during last third of a game. There's a reason why the phrase "birds of a feather" gets invoked a lot.
- A friendship with Darcy oddly enough. Not only does telling him the truth about why you were picked for the mission: (You didn't volunteer for it, it was assigned to you) make him feel better about the whole thing, but he shows his affection with things like photoshopped photos of the two of you in a Buddy Cop movie. Even after you go rogue, Darcy states, if you're his friend, that, he's going to look for you, but he's going to do the right thing and bring you in alive. And, if Mike surrenders, Darcy will bring him in unharmed to explain himself. When picking Mike up, Darcy is uncharacteristically subdued, doing his job with a sigh.]]
- A slightly strange one; if you hire Steven Heck to provide fire support during the Taipei subway mission, he sounds positively overjoyed.Mike: You know... there could be a lot of bad guys down there. If you wanted to help me take 'em out, well, I wouldn't say no.Steven: (Reputation +1) Really?! You mean it?! Oh, Mike, you don't know how much that means to me!
- The end of the Tapei arc if you're friend with Steven is this and Black Comedy. A Halbech representative came and offered him 5 million dollars for pointing Mike as the one who was the assassin hired to kill President Sung. Steven's answer? Snipping off a few fingers and setting the guy on fire.
Heartwarming / Alpha Protocol