After Voyager passes near a spatial rift, Chakotay is injured in Engineering, leaving his body in a state of temporal flux. After receiving treatment in sickbay, he inadvertently gains the ability to pass through rifts in time that are scattered throughout the ship, enabling him to walk into different stages of Voyager's history over the past seven years.
While chasing a renegade Maquis ship in the Badlands, the USS Voyager and the Maquis ship they are chasing are pulled into a vortex, which sends them instantly to the Delta Quadrant. However, after the destruction of the device that transported them to the Delta Quadrant, the crew of Voyager and the crew of the Maquis ship must join together to fight their way back to their home in the Alpha quadrant, which is many years away. They will meet many foes and many obstacles along the way, but they will also bond as a crew, between those of the Maquis and those of Starfleet.