After months on the run from the Cylons, things are beginning to wear thin on the Galactica. Chief Tyrol has permanently grounded yet another Viper because it’s too badly damaged to fly again, dwindling the Viper fleet to a precious few. Helo is given the cold shoulder by several of the new nugget pilots at a card game because he’s a "toaster lover". This even causes a fight to break out when Starbuck--enraged by her snide comments about Helo’s love for Sharon--pounds Racetrack’s head against a table. Sharon is again the subject of another fight, this time between the Chief and Helo. In the CIC, Dee is injured when her console unexpectedly explodes in her face. The normally cool and collected Mr. Gaeta blows up at Tigh when the XO commands him to get the problem fixed, and Adama begins to realize that the current situation--with everybody constantly on duty without a break or relief--is starting to grind his crew down.

Yet the Galactica has bigger problems once an investigation into the exploding console is launched. Baltar, working with Gaeta, discovers the presence of a Cylon virus within the Galactica’s computer. The virus first took hold back when Tigh ordered the computer systems to be networked in an effort to find the missing fleet back in "Scattered". In the following weeks the virus has broken down all of the firewalls that Gaeta installed as a protective measure and is now assuming control of vital operations aboard the Galactica--including communications, which it used to fire off an unknown message into the depths of space. When Helo--under Adama’s orders--brings news of the virus to the imprisoned Sharon, she recognizes what the virus truly is: a vanguard to an all-out attack by a massive fleet of Cylon raiders.

Flight Of The Phoenix refers to the Blackbird project Chief Tyrol is working on throughout the episode. With so many Vipers being grounded due to damage, and nothing to replace them, the Chief decides it’s time to try building a new Viper. At first, his pet project is met with much skepticism, even among his own flight crew. But soon, the entire ship joins in with helping the Chief to complete the ship: Starbuck becomes a vocal supporter of the project, helping out wherever she can, while Dee oversees installing the communications, and even the overly cynical Tigh gives Tryol a much-needed helping hand. In the process, by the end of this remarkable and touching episode, the morale of the Galactica crew is completely reborn, much like the Phoenix, from the ashes of their defeat by the Cylons at the Twelve Colonies.