Alpha Protocol is the only Obsidian RPG in which the player is a spy rather than a fantasy hero, and it is built around a systemic secret: every conversation choice affects NPC relationship values that determine not just optional interactions but main story events. Characters who like Thorton provide intel; characters who dislike him withhold it. The game can be completed with significantly incomplete information if relationships are mismanaged.
Handler Mina Tang has a file — accessible through specific hacking sequences in her personal quarters in the second visit to the safehouse — that predates the game’s events and describes Thorton as an Agency asset targeted for a specific mission profile. The file was written before Thorton was recruited and contains details about him that the Agency should not have had before his enlistment.
Obsidian built an implication that Thorton’s recruitment was not accidental and that Mina’s assignment to him was calculated rather than coincidental — a thread the game never resolves because Alpha Protocol did not receive a sequel.
The Agency conspiracy extends deeper than the game’s main questline reaches. Mina’s file is the evidence trail’s beginning with no documented end.
The detail work the devs put into areas most players never visit is what separates great games from good ones.
I’ve put 200 hours into this game and never caught this. The developers really reward the obsessive players.