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.

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.

At the start of the game, players can choose Thorton's agent history; options include Soldiers—which focuses on using heavy firearms, Tech Specialists—which have an arsenal of gadgets to use, and Field Agents—which encourages the use of stealth.

[7] Weapons can be extensively customized; options include the addition of a scope to improve shooting accuracy and the use of phosphorus ammunition to burn enemies.

In missions, players can approach their objectives in a variety of ways; they can directly confront enemies using the four weapon classes—submachine guns, pistols, assault rifles, and shotguns—and use gadgets such as grenades, flashbangs, and detonated mines.

[12] By choosing the correct dialogue options and completing certain gameplay challenges, players can earn small combat enhancements called Perks.

Thorton's colleagues are his handler Mina Tang (Adrienne Wilkinson), superior Yancy Westridge (Gary Anthony Williams), and veteran Alpha Protocol advisors Alan Parker (Michael Bell) and Sean Darcy (Andre Sogliuzzo).

Alpha Protocol is a highly classified black ops agency whose existence remains unknown to many—even those in the highest echelons of the United States government—as a means to operate outside of the confines of government oversight.

Recent inductee Agent Michael Thorton is given his first assignment; the assassination of Sheikh Ali Shaheed, the leader of the Saudi Arabia-based terrorist group Al-Samad, which used American-made missiles to shoot down a civilian airliner.

Shaheed's intel reveals three key locations tied to the conspiracy; Rome, where an Al-Samad cell has been activated; Moscow, through which the missiles were routed; and Taipei, where Taiwanese President Ronald Sung is under threat of assassination.

Thorton deduces that Halbech's plan is to raise global tensions and cause a new cold war, turning the world into its private marketplace.

In Rome, Thorton meets Madison Saint James, with whose help he discovers the private security firm Veteran Combat Initiative (VCI), which is run by Halbech's former security chief Conrad Marburg, who is planning a false flag operation to blow up a museum to influence harsher anti-terrorism legislation in Europe using Al-Samad as a scapegoat.

During his investigation, Thorton can encounter German VCI-affiliate mercenary SIE, and Sis, a mute in-service to Albatross, the leader of the G22 paramilitary group.

In Taipei, Thorton uncovers a plot by Omen Deng of the secret police to assassinate Ronald Sung and incite riots at a political rally to provoke a conflict with the United States.

With aid from Triad leader Hong Shi, and/or G22, and Steven Heck—a psychotic man claiming to work for the CIA—Thorton counters an assassination attempt by Deng and obtains a disk containing the plot.

When the disk is analyzed, a security protocol starts to erase data, forcing the player to choose to save files detailing either the assassination or the riot instigation.

Additionally, Thorton can learn that the real assassin in Taipei was Scarlet Lake, who is in Leland's employ, and he may choose to either execute her for justice, let her go, or invite her to team up with him.

Escaping into a bay on a motor yacht (potentially with a number of allies), Thorton considers his next move and wonders whether his life will continue to be exciting.

[24][25] While layoffs at Obsidian were avoided, the cancellation of Dwarfs forced the studio to give Sega the intellectual property rights to Alpha Protocol.

[22] The team also struggled with designing stealth for the game due to their lack of experience and technical difficulties caused by the Unreal Engine 3.

A planned female version of Micheal Thorton was canceled in order to save money; the team would have needed to change dialogue and create new animations for the character.

[29] The development team were inspired by pop culture spy icons such as Jack Bauer and James Bond; the game was a "Jason Bourne adventure" with some over-the top-characters similar to those in Kill Bill.

[26] They also took inspiration from other games, including Deus Ex, System Shock 2 and Fallout, TV series like Burn Notice,[26] as well as films such as Syriana, Ronin, and The Good, The Bad, and The Ugly.

[34] This resulted in a substantial rewriting and repurposing of the plot; player choice was given more importance, intertwining of gameplay and reactivity became a forefront design philosophy, and the core and motivations of several narrative threads were changed.

[41] In June 2019, Sega halted the sale of Alpha Protocol across all digital outlets, including Steam and the Humble Store, due to the licenses of several music tracks used in the game having expired.

[49][53][47] Rich McCormick from PC Gamer called the combat "simplistic" and the gunplay "floaty", but he was impressed by the weapon customization system's complexity and extensiveness.

[52] Juba was disappointed by the lead character Michael Thorton, who he felt lacks a personality, and that the dialogue stance system is only capable of providing clichéd choices.

[54] Tan called it a strange hybrid with disappointing and average gameplay, and provocative RPG systems, and described the game as a divisive title.

[56] Phil Savage called the game "a wonderful mess, full of great ideas, but hampered by the sort of behind-the-scenes development troubles".

[57] Anthony Burch from Destructoid praised the game's sense of humor, ending variety, and the combat system, in which he stated its "brokenness" becomes fun.