Michael Thorton, a name without a past, is Mike's new identity after joining Alpha Protocol . As an agent of Alpha Protocol, his mission is to assassinate the leader of Al-Samad known as "Shaheed", who destroyed a passenger plane in the Middle East. However, this task becomes much more complicated when dealing with terrorists.
Alpha Protocol combines elements of role-playing games and shooters, similar to Deus Ex. The player takes control of Michael Thorton after his initiation into Alpha Protocol, choosing one of four classes (Soldier, Field Agent, Tech Specialist, Freelancer) which determines his past. The player can also customize Mike's appearance, but with limitations.
The game progresses by sending the protagonist to Rome, Moscow, and Taipei in any order, where he prepares for his next mission. The player has access to a TV to keep up with current events, a weapons locker, a computer to check email, and the "Clearinghouse" - a black market service where Mike can sell items and buy gear.
The conversation system is similar to Mass Effect 2, offering various choices without fully spelling out the sentence. The player's choices greatly impact how enemies view him, making some interactions easier or more difficult. The Clearinghouse also offers ways to make a mission easier.
Mike's actions affect his relationships with others and change how enemies perceive him. His attitude can influence how people react to him. Being suave towards Mina may seem like a good idea at first, but she prefers a professional approach.
The game offers different ways to complete missions, from using guns to stealthy take-downs or hacking. Each task involves mini-games that increase in difficulty as the player progresses. The player earns experience points and upgrades their skills, unlocking new abilities and special perks.