Metathrone Project begins with the discovery of an ancient and mysterious artifact by a group on an archaeological expedition. Relics over a million human years old. Scientists have been able to establish that this is Noah's Ark for an alien race that attacked Earth and is trying to conquer the planet. People went to war with aliens, trying to defend their home and throw off invaders from another galaxy.

The gameplay is typical of a first-person shooter with a sci-fi setting. The action takes place in the future, so the environment is presented in a cyberpunk style. The stealth system allows gamers to move around the location unnoticed and instantly eliminate opponents from behind. Enemies have alertness levels: calm, tense and combative. If the main character has been spotted, then opponents will begin to call allies for help, so sometimes you should silently eliminate opponents.

The project has 13 consecutive levels. The plot is minimal, and the emphasis is on gameplay and dynamic shooting. The central character uses several types of firearms, such as sniper and automatic rifles, pistols, SMGs and consumables in the form of grenades. During prolonged shooting, there is a scatter, forcing the user to control the direction of the bullets or periodically stop for accurate hits.