The game features some mission types composing of multiple parts, such as alien shipping route terror attacks in which the first part is a battle of the upper floors of the ship while the second part takes places in the lower decks of the ship (all parts must be completed for these missions to be successful, and soldiers lost in previous parts do not appear in later parts). Underwater battles use the same physics as the ground ones but certain weapons cannot be used on surface/land missions. The second part, 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. The first is the real time-based GeoScape, a global view of Earth where the player views alien and X-COM craft and bases, can hire and dismiss staff, buy and sell vehicles, weaponry, ammunition and items, and build and expand bases.

Just like X-COM: UFO Defense, the game consists of two parts. This is also used as a plot device all of the alien technology from the first game is unusable in salt water, forcing the player to capture and develop new technology. X-COM: Terror from the Deep takes place mostly underwater, with base-building and combat all being submerged beneath the waves. It is a sequel to X-COM: UFO Defense and the second game of the X-COM series, this time taking the war against a renewed alien invasion into the Earth's oceans. X-COM: Terror from the Deep is a strategy video game developed and published by MicroProse for the PC in 1995 and for the PlayStation in 1996.

Tech tree xcom enemy within