As tensions between the Federation and the Cardassians grow, Picard is ordered to leave the U.S.S. Enterprise to lead a top-secret mission. Beverly and Worf are also "reassigned" and begin rigorous training sessions with Picard, although only the captain knows the nature of their upcoming task. Among the crew, speculations about whether Picard will return arise when a now commanding officer, Captain Jellico, is assigned to take over instead of Riker. Jellico adds to everyone's anxiety by quickly implementing several major procedural changes that disrupt their daily lives.
Jellico is especially hard on Riker and Geordi, which naturally creates a great deal of tension. Troi uses her position as counselor to plead for a period of readjustment, but Jellico disregards her input, coldly insisting the situation with the Cardassians demands immediate action. Later, in a conversation with Picard, Jellico says he feels war with the Cardassians is unavoidable, and that he doubts Picard will ever return to the Enterprise. The ship is now his, and he plans to run it his way.
When Picard, Beverly and Worf finally embark on their mission, Picard is able to relay the enormous gravity of their situation. The Cardassians are rumored to be developing metagenic weapons — genetically engineered viruses that destroy all living things in their path — on an abandoned planet called Celtris III. Picard and his team have been ordered to locate these weapons and destroy them at any cost.
Back on the Enterprise, Jellico meets with Gul Lemec, a Cardassian leader, ostensibly in hopes of averting war. However, Jellico does everything he can to enrage Lemec, making him wait for over an hour and acting unreasonable once the meeting begins. He engages Riker and Troi in this "good cop, bad cop" game, hoping to intimidate the Cardassians into abandoning their plans. But Jellico's own plan appears to backfire when Gul Lemec reveals that he has information regarding the secret Federation mission.
On Celtris III, Picard, Worf and Beverly survive a difficult trek over the rocky, barren planet and finally arrive at their destination — a sealed cavern. They devise a plan to break the seal and it goes off without a hitch. However, once inside, they find nothing there. Realizing the cavern is a trap, they run to make their escape just as several armed Cardassians attack them. Beverly and Worf escape, but Picard is kidnapped and returned to Cardassian leader Gul Madred, who informs him that he must answer all questions asked of him or he will die.