In a surprising twist, Voyager finds a Federation Starship when answer a distress call. They learn this ship, the Equinox, was also pulled into the Delta Quadrant by the Caretaker. The Equinox is under attack by nucleogenic life forms from an unknown interspatial realm. Voyager extends its shields around both ship, which momentarily protects them both.
In trying to learn why the Equinox was under attack, they learn the Equinox' crew's dark secret, which turns out to be directly related to the interspatial aliens. Worse, they find the ship's Captain will do anything, and sacrifice anyone, to get his people home - even if it means sacrificing Voyager and its crew.
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.