In Cosmic Epsilon, players control a humanoid robot tasked with defending Earth from the invading Epsilon Empire. The gameplay alternates between flight mode and humanoid mode, allowing players to navigate through various levels while engaging in combat against alien forces.

The storyline of Cosmic Epsilon revolves around the urgent mission to repel an alien invasion, with players taking on the role of a robot hero who must blast through waves of enemies to save humanity.

Cosmic Epsilon stands out with its innovative use of 3D technology for the NES, providing a unique visual experience for its time, along with its engaging gameplay mechanics that allow for versatile combat strategies through the use of homing missiles and a chargeable Vulcan beam.