The project was mostly inspired by iconic spy characters such as Jason Bourne, James Bond and Jack Bauer, and by films including Syriana, Ronin and The Good, the Bad and the Ugly. While Obsidian co-founders Feargus Urquhart and Chris Jones came up with the concept of an 'espionage RPG', no one was assigned to lead the project until early 2008. The game's development began in March 2006 after publisher Sega approached Obsidian for a new intellectual property role-playing game. The game features extensive customization and a dialogue stance system that allows players to select dialogues based on three different tones. Played from a third-person perspective, players can confront enemies using firearms, gadgets, martial arts and stealth.

Throughout the game, players must make many choices that affect the narrative. Thorton becomes a rogue agent and must unravel an international conspiracy to stop a war. The player assumes control of agent Michael Thorton, a new recruit at a clandestine United States agency called Alpha Protocol, which is given unlimited resources to conduct covert operations on behalf of the government. Alpha Protocol is a 2010 action role-playing game developed by Obsidian Entertainment and published by Sega.

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