Nucleus is a puzzle-based shooting game with a dual stick control system similar to Robotron: 2084. Players are tasked with ridding a host body of a virus infestation, moving through the body's three main biological systems, the digestive system, the circulatory system, and finally the nervous system, culminating in a final battle in the brain.The basic game consists of shooting bacteria or progressively larger and larger viruses, which break down into smaller viruses when shot, or if left alone combine themselves into ever larger viruses. Each level also has a number of cells which clump together and interact in a physical manner, the players can move them around and manipulate them with a traction beam to construct barriers to hide behind or to block of parts of the dynamically changing levels.