Voyager attempts to create a Borg-like transwarp conduit with the help of Seven of Nine. During the first test, things go wrong and Torres must eject Voyager's warp core.
Torres and Paris are sent in a shuttle to retrieve the core, but find ships of the Caatati, a people ravaged by the Borg and with little to live on, about to salvage the core. The Caatati fire on the shuttle severely damaging it, but Paris and Torres are able to beam out into space before the shuttle explodes.
Janeway must negotiate back the core from the Caatati and find the two missing crew before they run out of air.
During her time with Paris floating in space, she realizes she has succeeded in passing through her Klingon Day of Honor, an annual day of self examination, and can now openly express her feelings toward him.
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.