Michael Thorton's past is shrouded in mystery, as he has joined Alpha Protocol , a clandestine service without ties to the US government, specializing in covert operations to protect home and country. His mission: Assassinate Al-Samad leader "Shaheed", responsible for destroying a passenger plane in the Middle East. However, life is never straightforward, especially when dealing with terrorists. In the end, Shaheed is just the beginning of a greater conspiracy, and it's up to Mike and the player to unravel it.
Alpha Protocol combines elements of role-playing games and shooters, bearing similarities to Deus Ex. The player controls Michael Thorton after his initiation into Alpha Protocol, with the option to choose from four classes: Soldier, Field Agent, Tech Specialist, or Freelancer. This choice affects Mike's past and pre-defined skills before the game starts.
The player can customize Mike's appearance at certain locations, including facial features and clothing, but has limited options. The game begins with a mission in Rome, Moscow, and Taipei, allowing the player to select their next destination and prepare for it.
During missions, the player fulfills objectives while keeping an eye out for money bags or ways to acquire more resources. The Clearinghouse, a black market service, offers gear and upgrades for sale, but the player must earn the money himself to avoid detection. The conversation system is similar to Mass Effect 2, with limited time choices that affect relationships and outcomes.
The player's actions have consequences, influencing how enemies and allies perceive them. News of their actions spreads globally, making some encounters easier or more challenging. The Clearinghouse also provides ways to aid in missions, such as bribing guards to avoid work.
Dealing with situations can be approached through various means: stealth, hacking, lock-picking, or brute force. Each approach involves mini-games that increase in difficulty as the player progresses. The player earns experience points for each action, allowing them to level up and upgrade skills like "Stealth" or "Assault Rifles".
Upgrading skills unlocks permanent bonuses and special abilities, such as increased awareness to detect enemies through walls.