Lovecraft, including the appearance of the Deep Ones (one of the alien races, the Tentaculats, is even described in-game as 'not even the depths of a Lovecraftian nightmare could spawn such as this indescribable creature' ). While the aliens and overall atmosphere of the original game was influenced by extraterrestrial life in popular culture, TFTD has a darker theme influenced by the works of H.P. Resource management is also present, as the player must hire and dismiss staff, buy and sell vehicles, weaponry, ammunition and items, and build and expand bases. Underwater battles use the same physics as the ground ones, even as many of the underwater weapons can be used on ground. The BattleScape is used for combat between squads of aliens and humans, and takes the form of a turn-based battle from an isometric view.

Here the player views alien and X-COM craft. The first is the GeoScape, a global view of Earth. However, the difficulty level has been substantially raised and there are a number of new features. The only time the game moves onto dry land is for terror site missions (when the aliens attack a port, ship, or island). Terror from the Deep plays out underwater, with base-building and combat all being submerged beneath the waves.

Terror from the Deep is set in 2040, decades after the first Alien War was won, when a mysterious new alien menace begins to emerge from the Earth's own oceans.

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