Battle of the Ionian Nebula
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Events leading up to the battle
During the power outage Saul Tigh, Galen Tyrol, Samuel "Longshot" Anders, and Tory Foster begin to aimlessly wander the halls of Galactica muttering the lyrics to a mysterious song, having heard it in their heads for the past few days. When all four arrive in the same room and see each other, they realize that they are actually Cylons themselves. When the alert is sounded, they resolve to continue serving in the roles they did when they believed they were human. Tyrol returns to the flight deck, Anders heads for his Viper, and Tigh and Foster go to CIC and return to the sides of their Admiral William Adama and President Laura Roslin.
During the scramble to launch the alert Vipers, Lee Adama, now a civilian after resigning from the military just before the trial of Gaius Baltar, returns to his quarters to retrieve his helmet and flight suit and join the fight. While intercepting the incoming waves of Raiders, he picks up an unknown contact on his Viper's DRADIS and breaks formation to investigate. The unknown contact is intermittent and toys with Adama until it pulls alongside him and reveals itself to be Kara Thrace, alive and flying a spotless Viper Mark II. Thrace claims she has been to Earth and that she will lead the Fleet there (TRS: "Crossroads, Part II").
Civilians under attack
Galactica's Vipers and Raptors are able to stop the main force of 200-plus Raiders, but the Cylon reserves manage to break through the Colonial lines. Outgunned and with the civilian ships requiring time to spin up their FTL drives, Admiral Adama orders all available pilots and ships to launch, including inexperienced nuggets like Samuel Anders and Diana "Hardball" Seelix.
The battle floods over the drifting Fleet, Vipers and Raiders dogfighting among the ships while Galactica puts up anti-aircraft artillery (AAA) and fires its primary batteries at the Raiders and basestars. A damaged Raider collides with Pyxis, destroying the liner and the 600 people aboard. The Cylon basestars launch a barrage of over 50 missiles, half of them targeting the civilian ships. Adama orders all Vipers and point defense batteries to concentrate on protecting the civilians, since Galactica can withstand the damage. Two missiles hit Zephyr, resulting in severe damage to its ring section and many causalities, and another missile strikes Astral Queen, breaching the forward section of its hull. A missile bound for Colonial One is successfully intercepted by Seelix.
When Anders maneuvers behind a Raider chasing Seelix, it abruptly turns around, scans him with its single red eye, and breaks off when Anders' own eyes flash red in a Cylon friend or foe identification signal. To the amazement of the Colonials, the other Raiders return to their basestars and the Cylons spin up their FTL drives to jump away. Adama seizes this opportunity and orders the Fleet to withdraw (TRS: "He That Believeth In Me").
The Cylons now suspect that the Final Five reside within the human fleet. Since the Raiders broke off the attack of their own volition, a Cavil decides to have them lobotomized to remove part of their free will. The Four and Five models support that decision, but the Two, Six and Eight models do not. When Sharon Valerii sides with Cavil, he takes that as the deciding vote and has the Raiders lobotomized. In retaliation, a Six named Natalie, now advocating a search for the Five, removes the devices that enslave the Centurions, turning them on Number One's faction (TRS: "Six of One"). This marks the beginning of the Cylon Civil War which forces the rebels and humans to work together in an alliance that ultimately leads to the discovery of Earth and multiple victories over the Ones and their forces.