A transporter malfunction causes the Doctor's mobile emitter to fuse with some of Seven of Nine's Borg implants. When the emitter assimilates a crew member, Seven becomes aware of a Borg presence on Voyager. Worse, the Borg are also alerted to Voyager's presence.
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.