An alien missile with artificial intelligence takes over The Doctor's systems, and insists that it be allowed to complete its mission of mass destruction.
Seven is recruited by Captain Braxton of the 29th century timeship Relativity to go back in time and stop an unknown culprit from destroying Voyager.
Captain Janeway relates the story of her distant ancestor, Shannon O'Donnell (Kate Mulgrew in a dual role), and her involvement in the construction of Earth's "Millennium Gate". She meets and falls in love with Henry Janeway - the one man standing in the way of the Gate's construction.
After encountering a damaged Malon freighter, a repair crew from Voyager tries to contain a toxic chemical leak that threatens a nearby inhabited planet.
After Paris and Torres tie the knot, the ship and its crew start to disintegrate on the molecular level.
When an intense gravity well causes Tuvok, Paris and The Doctor's shuttle crash on a barren planet, they befriend a female alien who had also crashed there years earlier. As the months pass, they give up hope of being rescued. However, aboard Voyager, only a few hours have elapsed.
The crew of Voyager discover a simulation of Starfleet Headquarters being run by Species 8472, being used as a training ground in preparation for an assault on the Alpha Quadrant.
Picard tries to save his newly-discovered son from the retaliation of a vengeful Ferengi whose only son was killed by Picard during the Battle of Maxia many years before.