Riker finds out his former commander from the starship Pegasus has orders that entail more than what is revealed to Picard, who thinks the Enterprise is en route to recover the lost ship. And Riker is ordered to secrecy.
In an attempt to preserve a race of people on a planet being bombarded by storms that would kill them, Worf's foster brother violates the Prime Directive, leaving the Enterprise crew in a difficult position.
Dr. Crusher meets the man in her dead grandmother's life when she tries to put her affairs in order, whom one of the local people warn her to stay away from by not lighting a candle that has been lit for generations.
A mission of the Enterprise as seen through some junior officers who are up for promotions, as questions of duty and honor arise among some of them, such as a Bajoran whom Worf has designated to be promoted to operations.
Data is sent to follow a probe that has drifted off course and crashed on a primitive planet, only to crash on the planet, himself, with no memory of any event prior to crashing on the planet's surface.
Investigating a rogue comet that's been traveling throughout the universe for over 87 million years, Picard discovers alien beings within the comet, which infest the computer systems on the Enterprise, as well as Data.
Strange images begin appearing throughout the ship's decks and holodecks. Data and the rest of the crew begin to investigate only to discover that the ship's computer itself is exhibiting the strange behavior as it begins to become self-aware.
Following her return from Advanced Tactical Training, Bajoran Ro Laren is sent to infiltrate the Maquis and finds herself torn between her loyalty to Picard and Starfleet, and her sympathy with the Maquis fighting "the good fight".