The player takes command of a ship (presumably a graviton) on an x axis plane to collect and shoot electrons at a spinning atom to obtain a new atom. For example, if the player has one electron circling, he or she would shoot another electron in place to make a hydrogen element. If the electron misses the target and hits the nucleus, the atom becomes unstable and blows apart, sending electrons flying around the game screen, and the ship needs to find safety behind barriers located in three of the four corners of the arena.
Atom is a timed game with a countdown timer in the upper left corner of the arena timed in nanoseconds (actually tenths). Once the timer reaches zero, the atom destabilizes and explodes.