In Nucleus, the player assumes the role of a "remote unit" that is tasked with eliminating viruses inside the human body.

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 beam to construct barriers to defend against viruses.

These include destroying a certain amount of viruses, surviving for a set duration, gathering power-ups, or achieving a score target.

Exploding protein bombs or angry nuclei exert a large force over a wide area, which can break the cell walls the player has constructed.

[4] A patch has been released which offers a new mode of play, Nucleus+, which speeds up the gameplay and modifies and adds new levels.