Captain Janeway recalls a 21st-century ancestor Shannon O'Donnel, involved in creating a seminal self-contained biosphere called the Millennium Gate on Earth on New Year's Eve 2000. O'Donnel must convince the last holdout, local bookstore owner Henry Janeway to approve the plan.

While Kim is serving as commander of Voyager, the ship receives a distress signal. When the away team, including the Doctor, goes to a planet searching for someone needing assistance, they find a mysterious object with artificial intelligence. After Kim beams the device onboard, the crew discovers it to be an intelligent alien missile. They attempt to separate the intelligence from the weapon to save the intelligence and neutralize the weapon. But, it links with the Doctor's program terrorizing the crew and requests it be allowed to complete its mission of mass destruction.