Alpha Protocol is an action role-playing stealth game developed by Obsidian Entertainment, their first title for an original intellectual property, and published by Sega. The game revolves around the adventures of field agent Michael Thorton. Agent Michael Thorton is the newest member of "Alpha Protocol", a clandestine service established to perform covert operations that cannot be traced back to the U.S. government. His initial mission is to assassinate the leader of Al-Samad, Shaheed, after an attack on a passenger aircraft in the Middle East. After capturing Shaheed—whom Thorton can either execute or release—the terrorist leader claims that Halbech, a defense contractor, sold him the missiles and gave him all of the necessary information to carry out the attack. After relaying the information, Thorton's position is attacked by a missile strike, and Thorton is presumed dead. Being contacted by a member of AP, Thorton is told that the group has been infiltrated by members of Halbech who want Thorton dead, to cover up the fact that Halbech provided the missiles to Al-Samad.
Alpha Protocol is played from a third-person perspective, allowing the player to see Thorton and his surroundings at all times. As Thorton is a trained CIA operative, the tools at the player's disposal include numerous firearms, hand to hand combat using Kenpo, and spy gadgets.