Warhammer 40,000: Inquisitor - Prophecy is a stand-alone expansion of Warhammer 40,000: Inquisitor - Martyr. The game is set in the 41st millennium, where the galaxy is in a constant state of war. The game takes place in the remote Caligari Sector, where players face new unexplained attacks by Aeldari warriors fleeing their dying Craftworld. The game also features the hideous Tyranids, slowly coming back from their hibernation, and a mysterious presence returning from the Warp on the long-lost "Martyr".

The game offers a new Tech-Adept Inquisitor class, which is a summoner that can enhance units in battles to help defeat enemies and complete investigations. The game has new and revamped gameplay elements, such as 2-4 player co-op missions, destructible environments, all previous enemy races and units, and the unique gore of the Warhammer 40,000 universe. The game also has a new campaign, with three new and stand-alone chapters, and new settings to explore. Moreover, the game introduces new enemy races, including the Eldar and Tyranids.