The Enterprise is en route to a briefing concerning the current situation along the border of the Cardassian-Federation demilitarized zone. Meanwhile, newly promoted Lieutenant Ro Laren arrives in Ten-Forward to attend a welcome back party after recently graduating from Starfleet Advanced Tactical Training class.
The Enterprise responds to a distress call from a Cardassian warship under attack by the Maquis, a paramilitary organization of Federation citizens who have taken up arms against the Cardassians. The Enterprise uses a spread of photon torpedos detonated between the Cardassian and Maquis ships, causing them to break off their attack and withdraw. Later the Enterprise has its rendezvous with Vice Admiral Alynna Nechayev's Excelsior-class ship and she expresses Starfleet's concern about the Maquis, who are jeopardizing the Federation-Cardassian peace treaty. She advises Picard that Starfleet has decided to infiltrate the Maquis using Ro Laren.
Ro finds her way to a bar where she is contacted by members of the Maquis. After verifying her cover story, they quickly accept her into their ranks. She forms a bond with Macias, who Ro obviously sees as a father figure. Alarmed by this news that the Cardassians are arming their citizens with biogenic weapons, the Maquis plan a preemptive strike, however, Macias points out they are critically short of medical supplies. Ro offers to steal the needed supplies from the Enterprise, which she manages with some covert help from the crew.
Returning to the Enterprise for a debriefing, Ro tells Captain Picard (Patrick Stewart) of the Maquis strategy and Picard plots to manipulate the militants' paranoia in order to set a trap for them, hopefully eliminating, or at least crippling, their organization. Although Ro is troubled by this, she returns to the planet and is able to convince the Maquis leadership to plan an attack on the convoy supposedly carrying the components for the biogenic weapon, so the Federation fleet can attack from nearby nebula. However, disguised Cardassian militiamen attack the community which the Maquis cell is part of, and Macias is killed. As he dies, he tells Ro his death is not important since other Maquis like her will step forward to carry on the fight in his place.
Shortly thereafter a very unsettled Ro meets with Picard because she’s having second thoughts about the mission, asking him to call it off, saying that the Maquis cell she belongs to isn’t all that militant and may not even rise to the bait of the decoy convoy. Picard decides to send the ship’s First officer Commander William Riker (Jonathan Frakes), back to the Maquis with her to keep an eye on her and assure nothing interferes with the mission.
The day for the operation against the convoy arrives and as the Maquis fighters close in on it, Ro decides she can’t go through with the operation. She fires a low intensity particle beam into the Nebula, exposing the Federation attack force, and the Maquis ships break off their attack, frustrating the Starfleet plan. With great regret, Ro asks Riker to apologize on her behalf to Picard and beams to another Maquis ship. Back on the Enterprise, Riker files his report with Picard in the captain's ready room, adding that Ro seemed very sure of her decision, seeming that her only regret was that she had let Picard down. Riker leaves as the episode ends with Picard looking forlorn at the betrayal of Ro.