Steven Heck isn't humanHe's a Malkavian. Would certainly explain his... personality quirks. And his fighting prowess. And his vast knowledge of secrets both real and imaginary.
G22 is an offshoot of an earlier iteration of Alpha ProtocolReally, this hardly even qualifies as WMG, as it's just short of outright stated by the game, but there's no real way of being sure. Alternately...
G22 isn't affiliated with Alpha Protocol at all...But they want people to think they are, as a facet of some sort of plan that will become clear in the second game.
Albatross is Sis' father...well, it's less creepy than the other possibility for how concerned with her well-being Albatross is. It might also explain why he allows someone he's so concerned about into the espionage world; it's the only way he can keep his job and his family.
Marburg has a crush on MikeIf Madison is your handler during the mission to Marburg's villa, she all but spells out that Marburg is Straight Gay. What she doesn't know is that Marburg is also a Depraved Homosexual, and Marburg puts Mike through the Sadistic Choice because he's jealous. If the player takes the necessary steps to prompt Marburg to stay, fight and die in Rome, it works because Mike's insults are enough to make it clear that he's not good enough to have a chance at getting into Mike's pants. Playing it the opposite way and turning Marburg, or at least parting with him on psuedo-friendly terms, gives him enough time and space to decide pursuing Mike, who is both half his age and doesn't seem interested, would be unprofessional and unbecoming, which are both things Marburg likes to avoid.
Alpha Protocol shares a universe with Modern WarfareHalbech Ending: Boy howdy did Mike make a mistake forgetting that "Halbech is going to cause a real war" bit...
Alpha Protocol shares a universe with Army Of TwoDalton secretly worked for Halbech; the Army's casualties and the hit on Senator Whitehorse were for Halbech's benefit. Likewise, Halbech funds the 40th Day attack on Shanghai. Both are Halbech destabilization plots Mike never got intel on and thus didn't stop before they were set in motion.
Every single one of Steven Heck's theories is actually trueSteven really is a CIA agent, but he has become insane after discovering the truth about everything. The CIA considered eliminating him, but decided to 're-assign' him to a 'super-secret division' because he's somehow still effective in furthering the CIA's agenda. Besides, nobody believes him due to his personality and lack of conclusive evidence, so they figure all those secrets are still safe.
G22 is front of Ancient ConspiracyMy guess is Illuminati. Albatross once mentions that G22 has agenda like any government. They don't seem as governmental organization because they are widely considered terrorists. So they work for some Ancient Conspiracy aiming to manipulate and control world governments from shadows. It could even make sense that this way Alpha Protocol is set in the same universe as Deus Ex!
The other NPCs are meant to reflect various future fates of Michael ThortonMany of the major named NPCs in the game are meant to reflect possible fates for Michael Thorton. Mina is Michael Thorton's original hope for the future before Alpha Protocol; the loyal US government operative, squeaky-clean yet still able to get their hands dirty to get the mission done. Albatross is a Michael Thorton yet to come, one who doesn't let the continued betrayal and disappointment of the espionage world wear down his ability to still have ethics and find his own causes to fight for. Marburg is the Michael Thorton who lets himself get worn down into an unfeeling, lethal automaton, a pawn of whoever will use him, a collection of skills without a soul to animate it. Scarlet is a Michael Thorton who goes the Marburg route but with more self-respect, a freelance operative that works strictly for the money but picks and chooses her own life and her own allies. SIE is a Michael Thorton who gives up on planning for the future as he accepts that he has no future, just unrestrained forward momentum charging from firefight to firefight, living only for the moment and enjoying the rush, a life of nonstop motion until it all suddenly stops with a final bullet in the head. Leland is... hell, the game explicitly spells it out with the ending where you can choose to work for Leland, then betray him, then replace him and become him. And Steven Heck is... well, he's Steven Heck.
Obsidian will get the Burn Notice license
SecuritySift is run by a cell of G22Which goes a long way to explaining how they know everything about everyone. The warehouse in Taipei was actually run by a different cell of G22, and they didn't realize who they were helping Mike go after until partway through the mission, and notified Albatross.
Senator Darcy would have been a villain in the sequelLeland learned of the existence of Alpha Protocol from Marburg and then used a unspecified government connection to get in contact with it. Senator Darcy's son is an Alpha Protocol agent. Sean Darcy describes his father as "selling himself out" to become president. In one of the endings, Senator Darcy profits from Halbech's schemes by using Madison's death to get an extreme security bill passed. And in any ending where Alpha Protocol is exposed, he uses it to score political points. Furthermore, if Albatross is your handler when you kill Sean Darcy, he says that his father might cause problems. My guess is that a sequel would have seen Senator Darcy become a President Evil seeking vengeance against Mike.
SIE is pregnant.If SIE "rescued" Micheal in the medical bay, she got a little Someone to Remember Him By from Micheal.
If Mike Leaves the Island via Boat, 3 Seconds after The End Scene, the Boat Hits a MineSeriously, with all the precautions in place, underwater mines would not be out of place.
One day, Play Boy Mike will have SIE, Scarlet, Madison and Mina together with him all at once.
In Some Paths, Sis got to see SIE have sex with Mike.
The "No One Knows Where the Grey Box Is" is a lie. The OPERATIVES, don't know, but other personel do.
The Halbech Data always ends up squashed by HalbechThere are always three ways you can sell Halbech data in the game. You can use it to blackmail Halbech, you can sell it on the black market, or you can send it to Scarlet. Now, Halbech has contacts in the black market and can probably buy the information right quick if you sell it there. And Scarlet is secretly working for Halbech, so she has good reasons to quash any stories you send her (though she acts otherwise). Bottom line, none of this corporate espionage can ever harm Halbech, except for the trivial cost of squashing the story.
SIE is a transsexual"Sie" is a word (well, relatively, as far as it's used at all) commonly used instead of "he" or "she" when referring to genderqueer persons, and despite being (supposedly) female, clearly suffers from a very serious case of Testosterone Poisoning. Combine this with constant comments about implants and the fact that her sexual assets don't really seem to belong on a woman of her body type (which is to say, huge and muscular), and suddenly that sex scene near the end gets a whole lot creepier (or funnier, depending on how you look at it).