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Alpha Protocol is a secretive organization within the United States government in the game of the same name. Little is known about it since it is highly classified. Members seem to be geniuses in their specific field. Michael Thorton joins the organization shortly after the game's events begin.
Alpha Protocol is both the name of a government organization and also the term used by agents that classifies them as "rogue agents" to outside intelligence agencies (agents that have gone "Alpha Protocol" are considered acting alone or are traitors, so if their operation is discovered or goes awry, no blame will fall upon the United States). Not many within the government are aware Alpha Protocol exists, and this separation from the majority of Washington bureaucracy and oversight is intended to protect the United States from accountability for Alpha Protocol's "rogue" operations.
The Alpha Protocol insignia has some interesting symbolism, based on its description in the records. The ring of stars and arrows represents patriotism and military might, the eagle's talon is strength, the serpent is either its enemies pursued or stealth and subterfuge, and the loose translation of the Latin phrase beneath it is, "Where No One Can Follow."
Alpha Protocol field agents are often responsible for something that's been nicknamed the "Yellow Brick Road." While the agency will provide agents with funds and tech needed for their assignment, agents are encouraged to build their own pool of funds and resources... ostensibly so that the source of funds cannot be traced back to the agency. According to records, this means that since Alpha Protocol's inception, almost every field agent has had to set up private safehouses, accounts, and armories for their own use... yet none of these can be directly accessed by the Alpha Protocol agency itself.
Records indicate one of Sean Darcy's operations in Burma (by the name of "Red Lantern") required him to "Yellow Brick Road" the mission, and his funds are still located in untouched accounts - according to briefings, the funds from the operation were intended as bribes, but never used. They've remained there ever since, accumulating interest, and it's a simple matter to redirect the interest payments to current missions.
Westridge himself has "Yellow Brick Road"ed operations as well. According to reports, he has (had) a long-standing grudge against a former KGB agent by the name of Alexi Dravic - Dravic had murdered many agents and ruined countless operations, enough to earn him the nickname "Red Baron of modern espionage."
Westridge has a number of Ops under his belt - one is an operation called "Running Gun Blues" in Colombia in the 1980s. A drug dealer, Marco Majia, decided to move into the military supply business, moving equipment to groups unfriendly to American interest... Westridge went undercover to gain his trust, but things didn't go smoothly (Westridge cites "overzealous DEA agents" in the files).
The information in Westridge's file is correct. If Alpha Protocol is uncovered (and it has been, several times, in a chain that looks like it dates to the early 1950s), the program is erased and begins anew under a different name and a different code for "rogue" agents. Previous names of the agencies include "G19" and "Deus Vult."
The staff for the black ops programs have an equally colorful history - one of the founders of the Agency was involved in authoring "Operation Northwoods" - a plan in 1962 to start a war with Cuba. One of the key steps in the plan: making it look like Cubans shot down a passenger plane when it was, in fact, CIA operatives doing it all along and framing the Cubans. Fortunately for the free world, this little plan didn't happen, but it's the means by which Alpha Protocol makes the world a safer place.
- Initial Graybox mission in the briefcase in the locker after the Hacking Tutorial.
- Conversation with Yancy Westridge before Orientation at Graybox.
- In the infirmary during Alan Parker's stealth challenge.
- Mail from Mina in Rome.
- Found on the computer in the room of the museum in Rome with the elevator that brings new guards.
- Email from Omen Deng before last mission
- In the room where you can contact Parker in the Infiltrate Alpha Protocol mission.
- Secret Fact: In the room just before the confrontation with Parker, after meeting your handler (along with a regular dossier if don't have 100% yet)