While observing the peaceful Ba’ku people on their planet, Lieutenant Commander Data (on secondment to the duck blind mission there) appears to malfunction, revealing the hidden presence of the joint Federation and Son’a task force to the Ba’ku. Admiral Matthew Dougherty requests the help of the starship USS Enterprise-E to help capture or disable Data. Admiral Dougherty’s allies, the Son’a, are a decrepit race using various medical techniques to cheat death, repeated face lift surgeries giving them a mummified appearance. After stopping Data, USS Enterprise captain Jean-Luc Picard becomes suspicious of Dougherty’s insistence that the Enterprise is no longer needed, and his crew investigates the cause for Data’s malfunction. They discover that the Ba’ku are technologically advanced but have opted to live in harmony with nature. Due to unique radiation or “metaphasic particles” in their world’s rings, they are essentially immortal. The Enterprise crew also begins to experience the rejuvenation effects of the planet; La Forge finds his eyes have regenerated, and he no longer requires implants, William Riker and Deanna Troi rekindle their long-abandoned relationship, and Picard develops a romantic relationship with the Ba’ku woman Anij.
Picard and his team discover a cloaked Federation ship containing a gigantic holodeck recreating the Ba’ku village; Data’s malfunction was due to a Son’a attack when he previously discovered the vessel. Confronting Dougherty with his discovery, Picard learns Federation officers and the Son’a plan to relocate the Ba’ku on the ship while they collect the planet’s radiation to further Federation science, destroying the planet in the process. Dougherty orders Enterprise to leave, but Picard tells Riker to let the Federation know what is occurring while he and others beam down to the planet and evacuate the Ba’ku.
The Son’a send out robotic probes to tag and transport the fleeing Ba’ku, while their leader Ahdar Ru’afo convinces Dougherty to allow two Son’a ships to attack the Enterprise. Riker is able to narrowly stop their attack and escape. With their plan exposed, Ru’afo insists that they must begin to harvest the radiation immediately, only to have Picard deliver a revelation: the Son’a and the Ba’ku are the same race. The Son’a are a breakaway faction of younger Ba’ku who a century previously, wanted to give up their bucolic existence and re-embrace the use of technology. Tensions escalated until they attempted to take over the colony, but when they failed the elders exiled them from the planet and its regenerative radiation, dooming them to perish slowly. The Son’a have spent the past century since trying (and failing) to preserve their lives through artificial means. This accounts for their altered appearance and reckless attempt to harvest the radiation. Dougherty is killed by the Son’a when he refuses to allow Ru’afo’s scheme to continue.
Picard, Anij, and several Ba’ku are transported onto the Son’a ship. After convincing one of the Son’a, Gallatin, to help him, Picard masterminds a ruse to transport Ru’afo and the Son’a to the giant holoship, delaying the destructive metaphasic process. Ru’afo discovers the trick and transports to the Radiation Harvester ship to start it manually. Picard follows him and manages to activate the self-destruct, destroying the Harvester and killing Ru’afo. The remaining Son’a are welcomed back by the Ba’ku who forgive their actions; Picard arranges a meeting between Gallatin and his mother. The Enterprise crew take a moment to enjoy their rejuvenated selves before returning to their mission.