"Flight of the Phoenix" is an episode of the reimagined Battlestar Galactica television series. This episode echoes the plot of the original series episode "The Long Patrol" where Starbuck tests out an experimental Viper with a new propulsion system. The title of this episode recalls the 1964 novel Flight of the Phoenix by Elleston Trevor.
Survivor Count: 47,853
Facing torn and conflicted feelings over their respective relationships with Boomer, Chief Tyrol and Helo have an argument which leads to a brawl in the hangar bay. To deal with the increasing stress in his personal and professional life, Tyrol begins to salvage parts to build a new fighter from scratch to replace a Viper he had to scrap. At first the rest of the deck crew are skeptical, but eventually the whole flight deck as well as some officers from the Galactica CIC joins in as the Chief's idea captures their imagination. However, finding metal to skin the ship becomes a problem; most of the scrap metal remaining has been tagged for use in Viper repair. At Helo's suggestion, the Chief uses carbon composites for the skin, making it stealth capable and invisible to Galactica's DRADIS radar system.
Meanwhile, isolated systems malfunctions on the Galactica start becoming more serious and frequent. It becomes clear that the ship is infected with remnants of the Cylon computer virus that it picked up when it became separated from the fleet (see "Scattered"). The Cylon virus is a heuristic learning program; it has spent the intervening time cracking the ship's passwords and testing its ability to control Galactica systems. While Dr. Baltar and Lt. Gaeta work to delete the virus, Commander Adama has Helo ask Boomer for help.
Boomer becomes alarmed when she recognizes that the virus code will soon shut down the Galactica defences and warns that a simultaneous Cylon attack is imminent. The virus could hijack every system on the ship, venting the ship's atmosphere to space and turning its guns on the civilian fleet. Hundreds of Cylon Raiders and Cylon Heavy Raiders jump in and hold formation as Galactica scrambles its outnumbered Viper squadrons to meet them. As the virus attack is about to culminate, Commander Adama is forced to trust Boomer, allowing her to "plug" herself directly into Galactica's computer and communications system.
Unexpectedly, Boomer broadcasts a virus of her own back to the incoming Cylon Raiders, rendering them helpless and easy pickings for Galactica's Vipers. The Viper pilots consider this "payback" for the way the Cylons destroyed Colonial forces in their initial attack on the colonies. Boomer is returned to her cell, possibly having won a grudging respect from Adama.