Overview: Endgame
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When you enter your safehouse for the Endgame portion of the campaign, you'll start up a conversation with Mina. If you have a positive reputation with her, then she'll be there in person; otherwise, she'll talk to you over your television set. The two of you will decide that you'll need to return to Graybox to look for incriminating evidence on Halbech, and also to put a stop to their evil ways. If your reputation is high enough, then at the end of the conversation you'll be able to romance Mina (by selecting the "kiss" dialogue option), which will grant you the Office Romance perk.

Depending on how you dealt with people during the campaign, you might have up to three contact missions that you can complete before heading to Graybox -- Contact Albatross, Contact Scarlet Lake, and Contact Sheikh Ali Shaheed. None of these missions will make much of a difference in the final mission. Some of your potential allies (like Omen Deng and SIE) will send you emails instead.

The mission Infiltrate Alpha Protocol is the final mission in the campaign, so only start it up once you've completed everything else.

"If Alpha Protocol thinks it's the only one with an army, they're in for a shock."