In the Middle East, a terrorist group shot down a passenger airliner. The attack was made using the latest American-made missiles. The agent Michael Thorton is assigned to investigate the case. He manages to get on the trail of the leader of the group, but suddenly he is removed from the job and betrayed by senior colleagues. Now, when the American government hunted him, Michael uses "Alpha Protocol" - a secret program that recruited him and begins to work to detect the conspiracy secretly.

Alpha Protocol gives you the ability to take control of Thorton with a camera from a third-person perspective (you can see all that surrounds you). The CIA trained Thorton, so at his disposal is possession of weapons of ranged and melee, as well as technical devices. The player also earns promotion points, which increase skills in using guns and give additional abilities.

Alpha Protocol provides the ability to interact with numerous characters in the game. Conversations take place in real time, thus giving to the player some time to answer in essential dialogues.