Lieutenant Commander Data (Brent Spiner) is temporarily transferred to an undercover mission observing the peaceful Ba'ku people. While on their planet, he malfunctions and reveals the presence of the joint Federation-Son'a task force observing the Ba'ku. Admiral Matthew Dougherty (Anthony Zerbe) contacts the USS Enterprise-E to obtain Data's schematics but adamantly states that the Enterprise is not needed. Captain Jean-Luc Picard (Patrick Stewart) decides to ignore those orders and takes the Enterprise to capture Data. After stopping Data, Picard becomes suspicious of Dougherty's orders that the Enterprise is not needed. His crew investigates the cause of Data's malfunction. They discover that the Ba'ku have advanced technology, but have rejected its use to live simpler lives. On account of a unique metaphasic radiation emanating from their planet's rings, they are effectively immortal. Dougherty's allies, the Son'a, are a decrepit race who use medical techniques to prevent death; their excessive use of cosmetic surgery gives them a mummified appearance. The Enterprise crew also begin to experience the rejuvenating effect of the planet; Lieutenant Commander Geordi LaForge (LeVar Burton) finds his eyes have regenerated and he no longer needs ocular implants; Commander William Riker (Jonathan Frakes) and Counselor Deanna Troi (Marina Sirtis) rekindle their long-abandoned relationship; and Picard develops a relationship with the Ba'ku woman Anij (Donna Murphy).
Picard and Data discover a submerged and cloaked Federation spacecraft containing a gigantic holodeck recreation of the Ba'ku village. Data's malfunction stems from a Son'a attack, received when he discovered the vessel. Picard confronts Dougherty and learns that high-ranking Federation officers and the Son'a secretly planned to deceptively move the Ba'ku to the spacecraft and forcibly relocate them to another planet, allowing the Son'a to collect the rejuvenating radiation (but poisoning the planet in the process). Dougherty orders the Enterprise to leave. Picard states the rejuvenating benefits of the radiation does not justify Dougherty's plans for the Ba'ku and violates the Prime Directive. He plans to alert the Federation of the forced relocation.
Picard is joined by some of the crew to help the Ba'ku escape from being abducted while Riker takes the Enterprise far enough from the Briar Patch to communicate the violation to Starfleet. The Son'a send robotic probes to locate and capture the fleeing Ba'ku. The Son'a leader, Ahdar Ru'afo (F. Murray Abraham), convinces Dougherty to allow two Son'a ships to attack the Enterprise. Riker defeats the attacking ships and the Enterprise escapes. Their plan exposed, Ru'afo insists upon harvesting the radiation source immediately. Picard, Anij, and several Ba'ku inhabitants are transported onto the Son'a flagship. Picard reveals to Dougherty that the Son'a and the Ba'ku are the same race and involving the Federation in a blood feud. The Son'a are a splinter faction of the Ba'ku who gave up their bucolic existence a century earlier to embrace the use of technology. They attempt to seize power but failed, and the Ba'ku elders exiled them from the planet, denying them the rejuvenating effects of the rings. The Son'a develop an artificial and imperfect means to extend their lives at the cost of disfigurement. Ru'afo kills Admiral Dougherty when he backs out of the plan and Ru'afo proceeds with his plan.
While Picard is escorted to be executed, he convinces the Son'a officer Gallatin to help him stop Ru'afo. Picard masterminds a ruse to transport Ru'afo and his bridge crew to the holoship and shut down the radiation harvester. Ru'afo discovers the deception and transports himself to the harvester spacecraft to manually restart the process. Picard follows and sets the harvester to self-destruct, which kills Ru'afo while Picard is rescued by the Enterprise. The remaining Son'a are forgiven and welcomed back by the Ba'ku. Picard arranges a meeting between Gallatin and his Ba'ku mother. The Enterprise crew take a moment to enjoy their rejuvenated selves before returning to their previous mission.