The player controls Jake, the protagonist of the game, and explores a large island stage. The game takes place in 2021, in which the United States has established an island facility called Nanomachine Island to research and develop nanotechnology for implementation in military and civilian life. To reach this goal, the United States collected the world's foremost scientists, analysts and businessmen and then formed a secluded community out of them. Through 20 years of technological gain, this world is the result. As Jake, the player's goal is to assist the daughter of a brilliant scientist in her quest to restore order to the island and its people by destroying the main computer which manages the activities of the nanomachines.
As Jake, a cyborg militant, the player will wield a plasma blade that has the ability to transform into numerous weapons (axe, broadsword, hammer, etc.), which are generated by the blade during combo attacks. The plasma blade also has the ability to grapple enemies from afar with a blue energy cord. Jake's body is metallic and features wings that can come out of his shoulderblades and allow him to glide. The wings also serve as a sort of "limiter release" for more powerful combos and finishing moves. Within the game world, the player will be facing the mutated inhabitants of the island which are referred to as "Orgamechs". There are many different types of orgamechs including humanoid, bug and dog types. The points system is a counter which racks up the amount of blood spilled after killing an orgamech. After the counter reaches certain amounts of blood Jake will receive extra health and energy as well as increases in the maximum amount of health and energy Jake has at his disposal.
Nano Breaker was developed and published by Konami and was produced by Koji Igarashi, famous for his work on the Castlevania franchise. Nano Breaker uses a modified version of the Castlevania: Lament of Innocence engine.