As the crew deliver medical supplies to the non-affiliated planet Rutia IV, a bomb goes off in a public plaza, injuring many bystanders. Dr. Crusher attempts to tend to the wounded against Captain Picard's orders to return to the ship, but her efforts are interrupted when she is abducted by a man using an unknown method of teleportation. Picard and the crew learn from the head of Rutian security, Alexana Devos, that the bomb and Crusher's abduction were by the Ansata separatist rebels who seek to become independent of Rutian rule, and will likely use Crusher as a hostage. After being denied the use of the Enterprise's superior firepower to seek and destroy the Ansata's base of operations, Devos orders severe interrogation of all known Ansata sympathizers, an act that the Enterprise crew find immoral. Without new information from Devos, the Enterprise crew investigate the teleportation technology and find that it is used to shift between dimension, allowing the Ansata rebels to surpass even force fields, and that if they are able to observe the teleportation, they will be able to pinpoint the location of the base. Wesley takes an active part in the analysis in order to help save his mother.
At the Ansata base, Crusher learns her abductor is Kyril Finn, the leader of Ansata. Crusher follows the Starfleet protocol of taking the "higher ground", and refuses to eat or otherwise cooperate with Finn. After several hours, Finn lets Crusher out of her restraints and requests that she help treat their wounded. Crusher discovers that the "Inverters", the Ansata teleportation technology, cause irreversible damage to the user's DNA, and that many of Ansata's sick are due to excessive use of the Inverter. Finn admits that the Inverter is their only weapon against the Rutian government. After more hours pass, Finn believes the Federation to be working with the Rutian government and launches an attack on the Enterprise, despite Crusher's requests to avoid harming her son. Ansata manage to plant a bomb on the Enterprise warp engine, but it is quickly transported into space by La Forge, but the distraction is enough to allow Ansata to appear on the bridge and abduct Captain Picard. With Picard as his captive, Finn uses the Inverter to come to Troi on the Enterprise and demand the Federation become involved in mediating the dispute, returning to the planet before security can arrive. Picard, learning of Crusher's situation, tells her to continue to work on gaining Finn's confidence to hopefully end the dispute peacefully.
Data and Wesley are able to use Finn's appearance to locate the Ansata, and Riker and Devos assemble their forces. After they transport into the base, the combined forces are quickly able to quell the resistance. Finn, as a last resort, attempts to execute Picard, but Devos kills him, believing that if Finn remained alive his imprisonment would spark more resistance while being killed in battle may elevate him to a martyr and reduce the violence in the short-term. When a young Ansata member attempts extract revenge on Devos, Crusher is able to convince him to drop his weapon, which Riker notes is a sign that there may be more fruitful discussions to resolve the issue in the future. The Enterprise crew returns to the ship, and Crusher reunites with her son, thanking him for his efforts in rescuing her.