The crew of Voyager discovers a simulation of San Francisco's Starfleet Headquarters being run by Species 8472 and used to practice launching an assault on Earth and the Alpha Quadrant. Species 8472 shape-shift into human form using regular doses of drugs.

Voyager uses new quantum slipstream technology in an attempt to return home, but a miscalculation by Kim causes the ship to crash into an ice planet. Fifteen years later, the sole survivors, Chakotay and Kim, have resigned from Starfleet and attempt to alter history to save the ship from disaster before Starfleet can stop them. They steal the Delta Flyer to send a message back in time and avert the catastrophe. However, Captain Geordi LaForge is determined to stop them at all costs.