Destroy All Humans! is an action game where players take on the role of Cryptosporidium 137, a Furon Empire agent tasked with collecting human DNA samples. Due to some experiments gone wrong, Crypto's clones have become inferior and he needs fresh genetic material from humans. The player must navigate through various levels, using his powers such as hypnosis, psychokinesis, and flying abilities to achieve objectives.
The gameplay is centered around completing story-based missions and collecting specific DNA samples while avoiding detection by the authorities. Crypto can disguise himself using the Holobob and use various Furon weapons like the Zap-o-Matic and disintegrator ray to overcome obstacles. The game also features a mothership where players can upgrade their character, save progress, and receive new missions.