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I always wondered: how do your allies escape the facility in the end? I've had every game end with Mina & me on a bout, but then there's still Scarlet, Steve and Sis.
Is this explained anywhere in-game?

Not in game however you can reason using what the game tells you about the different characters.
Sie, Steve and Sis knows where the facility is and thus should be able to get out either by themselves, or by calling in a chopper (Sis, Sie), so no problem here.
Scarlet might know where the facility is, (though probably not) but might not have the network to get out on her own, so she might or might not get away (though the credits sometimes say she got out).
Funnily enough despite Mina working there, she almost certainly don't know where the facility is, and once it blows up might not even be able to contact the NSA (her employer), so good call on taking her instead of Scarlet.

Personaly I always liked to assume that I gave the other guys room in the boat. Except for Steve of course.

Why not Steve? He could entertain you. I also like to think they're on the boat, as it's the one option that makes sense. I think Scarlet would have the netwerk to get extracted, though, as she has called in earlier a chopper for extraction. (The one who gets shot down.)

Steven could also decide to torture the local trout population in order to find his keys, or keelhaul me for using his full name. While fun, I have never really got along with him.
Guess that leaves Mina as the only one who can't get out on her own, which means she'll be in trouble on half my playthroughs. On one hand, she is the second most "good" person in the game (Madison being the only real "saint"), and is pretty much the only reason Mike has survived. On the other hand, she did originally help Mike to shut down AP, and after seeing what happens to surviving elements of similar programs (G22, Deus Vult, possibly even Steven), I'm not completely sure she wouldn't turn Mike in if given the order.

At least Scarlet can be bribed (and I really really don't want to leave a pissed woman with a sniper behind).

I've found it nearly unavoidable to take Mina with you. I just never could make the choices leading up to that.

I believe the only necesary choices are 1: don't romance Mina and 2: save Scarlet, though maybe my game was bugged. Leaving her to die would be too cruel I agree, though I wouldn't trust her after she uses you to take down AP. At least Scarlet is mostly honest.

My first playthrough I did just that: I didn't romance Mina, romanced Scarlet, and spared Scarlet. Still, I ended up with Mina on the boat.

Too bad for you I guess, though my first playthrough went worse. I didn't find Scarlet, which led to one of the most memorable scenes in the game, especially since I didn't know she was behind the failed assasination, too bussy being angry at Steven for framing me I guess (another reason to hate him). Good thing she is bribeable, and overal I kinda prefered that ending if only for having more of an impact.

Steve never framed me, because we're bros. ;-)

Lemme guess, you did not play a stealth character? Because his idea of a stealthy entry, coupled with what happens if you hack a computer for him, kinda made me want to pay Scarlet to kill him instead of the president. He's good fun though (and a nice parody of Mike, Bourne and "superagents" in general).

I only use stealth to get a better vantage point from which to unleash hell.