It is 700 years in the future and Voyager has become museum piece on display by Kyrian race, in the Delta Quadrant. They visitors there are told how Voyager and crew caused the civil war 700 years ago between the Kyrians and the Vaskans, which nearly wiped out the Kyrian race. They are told how Voyager wiped out millions of Kyrian, after taking the Vaskan's side.
However, this view of history becomes challenged when a scientist reactivates the Doctor's program; but can the Doctor prevail against 700 years of strongly held beliefs? The more he tries, the more strife begins to grow between the Kyrians and the Vaskans.
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.