When Voyager becomes stuck in some sort of gravimetric sandbar, one of Tom Paris' holodeck programs, "The Adventures of Captain Proton", which was running at the time, gets strange alien visitors who exist as holodeck like photons. The villain in Tom's program meets the aliens, and decides to go to war against them. This causes power surges on Voyager. To contact the aliens, the crew must interface with the aliens on the holodeck, meaning they must also face the program's maniacal villain, Dr. Chaotica!
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.