Three cadets from the Academy of Galactic Exploration become lost in a Hyper Bubble (hyperspace) mid-jump and must band together with an alien named Kulai in order to survive in an unfamiliar part of the galaxy. Kulai (unbeknownst to the cadets) is a Chalim priestess from a planet called Pyria, a planet that was strip-mined by a warlike race called the Triiad, led by the Pyran traitor, Paiyin. The sole purpose of the Triiad is to wipe out intelligent races, and in the process acquire raw materials from their destroyed planets to continually create new war machines using automated self-replicating factory ships called "Makers."

The Hypernauts, as they name themselves, cannot match the Triiad's firepower with their own so they must rely on stealth, wits and (occasionally) their modified 'mech suits' in order to escape the Triiad. They are based in an ancient abandoned exploration ship called the Star Ranger which is hidden in an asteroid field, the Star Ranger's obsolete AI is named Horten. For long range missions they use a four person shuttle called the Flapjack which like the Star Ranger is Hyper Bubble capable but has a much shorter range.
The Triiad have englobed the central region of the Milky Way Galaxy in a sensor net that can identify the destination point of any hyperspace jump passing out of it, so returning home would lead the Triiad directly to Earth. The Hypernauts must keep the location of Earth a secret and somehow try to warn Earth of the Triiad's existence.