Boomer, on a 24 hour pass, joins Athena, Boxey and Muffet in the the Galactica's rejuvenation center. Meanwhile, the bridge picks up a Cylon combat probe on their scanners and Blue squadron is launched to intercept. However, they soon realize that the force is much bigger and they launch all fighters. The Galactica locks down all compartments.
Apollo and Starbuck notice that the Cylons are not engaging the vipers. Two fighters break through. Apollo tells the Galactica that the ships are preparing to ram. One of the ships rams the bridge and the other destroys the port landing bay. On the bridge, Adama is severely injured. The Galactica has lost its long-range scanners and internal communications.
The fires in the landing bay threaten the Rejuvenation Center as smoke begins pouring in under the doors. The fire in the landing bay is out of control. Boomer attempts to open a jammed door into a adjoining supply cabinet. In sickbay, Cassiopeia learns the fate of Boomer, Athena and Boxey. Apollo visits his father in sickbay. Dr. Salik tells Apollo that there is a fragment lodged in the wall of his father's heart and that he can't operate until the power situation stabilizes. Adama wants to see Boxey and Athena. The damage control team is losing control of the fire in the landing bay area and the Rejuvenation Center is becoming increasingly smoky. Boomer manages to get the door to the supply cabinet open and everyone evacuated into the supply room just as the door the center explodes open. Boomer starts to work on the exterior door of the supply room when he notices that the door is extremely hot.
The fire is outside the door to the supply room. On the bridge, the Chief Engineer gives Tigh status of the fire in the landing bay. It is getting close to both the backup Energizer and the Solium tanks. If it reaches either one, Galactica is doomed. Apollo desperately searches for a way to get to the people trapped in the Rejuvenation Center. Apollo comes up with a way to use the Vipers to help fight the fires in the landing bay. Apollo, Starbuck and Sheba launch their vipers equipped with Vorton pumps to strafe the landing bay with the fire retardant. In the Supply Room, Boomer puts Muffy into the ventilation system so can alert Galactica to their location. The damage control teams start their mega-pressure pumps. Apollo, Starbuck and then Sheba each do a strafing run and manage to extinguish the fire for a time but it re-flares. The power drops continue aboard Galactica, forcing Dr. Salik to consider operating on Adama.
Tigh visits Adama in sickbay. Adama suggests using the vacuum of space to put the fire out even though Boxey and Athena might be killed. As Sheba watches from her viper, Apollo and Starbuck leave the airlock to set their explosive charges on the Galactica's hull. Apollo tells Tigh that Boxey trained Muffy to sniff out mushies so Tigh orders some to be placed in the airlock on the bridge. In the air ducts, Muffy apparently smells the mushies and changes directions. Tigh learns that the fire is out of control in five different areas and is dangerously close to the second energizer. Welker begins his heart operation on Adama. Muffy reaches the bridge. In the storage compartment, the smoke is getting thick. Omega attaches life masks and Tigh changes the message on Muffy's collar telling them about their efforts to extinguish the fire. Starbuck loses his grip on the hull but Apollo manages to catch him before he floats off into space.
Salik continues his surgery on Adama. Starbuck and Apollo finish setting the charges and make their way back to separate hatches. On his way back to Boxey and the others, Muffy sees a crewman trapped in another compartment. Muffy reaches the storage room with the life masks and the note. Muffy goes back into the vent as everyone moves to the other side of the compartment to await the explosive decompression. Apollo loses his grip but Starbuck launches himself at Apollo as the charges explode. The fire is extinguished. However, they have lost contact with Apollo and Starbuck. Sheba manages to find them floating together in space. Apollo gets the good news about his family.
In Sickbay Adama tries to console Boxey on the loss of Muffy. Apollo comes in to check on his father, sister and son and learns the news about Muffy but Starbuck has some good news too. Apollo thanks Boomer for saving his sister and son. Muffy has been badly burned saving a fireman in another compartment but he will be as good as new.