Sisko and his officers take the Defiant to a remote system in the Gamma Quadrant for a trade discussion with the Karemma representative, Hanok. During the talks, two approaching Jem'Hadar warships are detected. The enemy vessels target the Karemma ship, which flees into the gaseous, volatile atmosphere of a nearby planet. Sisko enters the dangerous area in pursuit, and the Defiant is blinded and buffeted by high turbulence. They employ an echo-location technique to find the other ships. But the pulse gives them away to the Jem'Hadar, who attack and cripple the Defiant. Dax goes below to help get the engines on-line, but a hull breach develops, endangering her and others on that deck.
After evacuating Sickbay, Bashir notices Dax trying to escape. Just then, the forcefield that protects her collapses, allowing the deadly atmosphere to enter. Sisko orders Bashir to seal off the area, but just as he does, the doctor steps inside to rescue Dax and drags her into the turbolift, trapping both of them. Meanwhile, on the Bridge, the engines come to life, indicating that Dax was successful. O'Brien arms two atmospheric probes with quantum torpedoes and the crew resumes its search for the Karemma vessel. However, a Jem'Hadar ship finds the Defiant and opens fire, damaging it severely before the Defiant destroys it.
The Bridge is on emergency power only, while Sisko is seriously injured. Kira discovers that he has a concussion, meaning she must keep him from losing consciousness or risk having him slip into a coma. In the turbolift, Dax and Bashir have only limited air remaining; while, in the Mess Hall, Quark is trapped with Hanok. Worf makes it from the Bridge to the Engine Room, where O'Brien and his engineers are working to restore the ship's systems. Then, the echo-location scanner picks up torpedoes heading for the Defiant. The ship manages to elude one, but the other embeds itself into the Mess Hall bulkhead — still primed to detonate — and surprising Quark and Hanok.
Quark and Hanok realize they must work together to diffuse the torpedo before it blows. Meanwhile, the engineers come up with a new plan to fire phasers through the Deflector Array — which will only be good for one shot. And as Sisko slowly slips out of consciousness, Kira risks killing him by injecting a stimulant.
In the Mess Hall, Quark and Hanok manage to remove the torpedo casing and deactivate the warhead. On the Bridge, Sisko awakens, indicating to Kira that she did the right thing. In Engineering, O'Brien locates the Jem'Hadar ship, which is lured to a decoy using the remaining atmospheric probe. Worf's team destroys the enemy ship with the Deflector Array and rescues the Karemma crew. Bashir and Dax are freed, and the repaired Defiant returns to Deep Space Nine.