After waking up in a high security medical facility with no recollection of how he got there, John Vattic's memory slowly returns through a series of playable flashbacks to his days as a civilian advisor to a military operation in Siberia. In the past, he worked with a group of soldiers known as WinterICE, attempting to locate an elderly scientist who has been conducting research into psychic powers. In the present, John attempts to piece together what he remembers and locate members of WinterICE in the hope that he can clear his name, work out what actually happened, and discover how he came to have psychic powers himself.

Second Sight is a 3D shooter with stealth elements. The player mostly controls John from a third-person perspective, though it is possible to switch to first-person view under certain circumstances. During the course of the game the player gets to use telekinesis, healing, charm, projection and possession powers and two types of psychic attack, plus a variety of weapons. Most situations can be tackled with stealth, mindless violence or psychic powers, or a combination of the three.