Battle of The Colony
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The Colonials begin a rescue mission, the most dangerous and daring offensive ever undertaken by Admiral William Adama and a skeleton crew, to rescue Hera Agathon, kidnapped by Boomer and taken to the Colony for experimentation (Islanded in a Stream of Stars).
The battle comprises of people, both rebel Cylon and human, who volunteer to stay aboard Galactica. There are only perhaps several hundred human or humanoid fighters, but fortunately the Cylons also add a few hundred Cylon Centurions to the attack and defense forces. The free Centurions are painted with red stripes to distinguish them from the otherwise identical Centurions on the Colony.
Racetrack and Skulls are sent on a reconnaissance mission in a Raptor. They find the Colony in orbit of a black hole and also find the only place that a ship can jump in and out safely: within a kilometer of The Colony: point-blank range for The Colony's weapons.
Galactica jumps in directly in front of the Colony, which opens fire with its gun batteries as it's too close for missiles or nukes for both sides. Galactica takes a pounding until Samuel Anders (now effectively Galactica's Hybrid) manages to hack into the Colony and shut down its Hybrids and their weapon control.
Galactica immediately launches her Vipers to engage the Colony's Raiders while the battlestar's Raptors jump directly from the starboard flight pod in a flanking position to board the Colony. The Raptor's jumps rip open the side of the flight pod, but safely arrive at the battle.
As Galactica's gun batteries fire at the Colony's gun batteries and Raiders, Admiral Adama orders flank speed on Galactica, ramming the battlestar's dense "alligator-head" bow into the Colony. The collision punchs a hole in the Colony's side, Galactica's bow effectively docked in the enemy ship. From Galactica's bow, Lee Adama leads a strike force of marines and Rebel Centurions into the Colony. Raptor strike forces led by Starbuck, Helo and Athena cut their way in elsewhere on the Colony's hull.
The fight is not without serious losses. Racetrack and Skulls arm their nukes aboard their Raptor but are killed when an asteroid hits their ship, punching a hole in the window and smashing their helmets.
Inside the Colony, both strike forces push onwards despite opposition from not only modern Centurions but older Model 0005 Centurions.
Starbuck's forces discover Boomer, who has retrieved Hera out of sympathy and because she feels she owes Adama a favor. She hands the child over to the rescue team without a fight, warning the team that their Raptors have been destroyed and cannot be used for escape. Fortunately, the battle plan was to abandon the Raptors and return to Galactica through her bow.
After Athena kills Boomer, Starbuck's team meets up with Lee Adama and his team. All retreat to Galactica's airlock to escape the Colony.
Cavil, Simon and a Number Five go on the offensive, leading a platoon of Centurions in a boarding attack on Galactica. Firefights break out all over the ship, with both sides suffering heavy casualties. Gaius Baltar and Caprica Six are among the many that help defend the ship from the boarders.
Helo is wounded by a Five. Hera runs away in the chaos. Athena goes after her at Helo's insistence. Laura Roslin, working in sickbay, senses Hera's return and chases after her as well in what becomes a parallel of the Opera House Prophecy, each person in turn part of a vision that protects the child from harm as she wanders through decks filled with gunfire and enemy forces. Caprica Six and Baltar eventually find Hera and take her with them to CIC, recreating their movement as seen in their visions, encountering the Final Five there, standing on the CIC balcony.
Cavil is captured in CIC. During an explosion, Cavil takes Hera hostage and plans to leave with her as he sees her as the only hope for his kind. Baltar successfully talks Cavil into a truce in exchange for Hera's life. Saul Tigh sweetens the pot by offering resurrection in exchange for the permanent true between humanity and Cylons. Cavil calls off his forces and the battle seems to end.
However, the truce is short-lived. Shortly after the Final Five begin downloading their knowledge of resurrection to the enemy forces, Galen Tyrol breaks the download and kills Tory Foster when he learns that she is responsible for the murder of Cally Tyrol. Believing themselves betrayed, the Cylons restart their attack, but after the Doral and Simon that joined him in CIC are killed, Cavil curses and kills himself. The Raiders resume attacking Galactica.
In space, another asteroid strikes Racetrack's Raptor and causes her dead hand to accidentally hit the launch button for the remainder of the nuclear missiles from Galactica and Pegasus to fire. All 8 of the missiles hit the Colony, badly damaging it and knocking it out of its orbit towards the black hole nearby--and pulling Galactica with it.
Admiral Adama orders Starbuck to jump the ship--anywhere. Without the coordinates to the Fleet's location, she realizes that the mysterious music played by her father forms FTL coordinates. She enters the coordinates and Galactica escapes as the Colony is sucked into the black hole and destroyed.
The toll of battle and her structural frailty are too much for the old battlestar. As she completes the jump, Galactica suffers a series of critical structural failures, breaking her backbone and permanently losing her FTL ability.
But Starbuck's coordinates take Galactica to a habitable planet, lush and filled with life. They name this planet Earth and, after retrieving the other Colonials at the rendezvous coordinates, the population of the Fleet is able to settle without concern.
The Rebel Cylons settle down with them and give the Rebel Basestar to their Centurions to find freedom and their own destiny.
Samuel Anders, now functionally a Hybrid, agrees to autopilot Galactica and the last of her charge into the Sun, destroying the ships and allowing humanity and the Rebel Cylons a fresh start, sans advanced technology.
It is not shown whether any of the Cylons on the Colony were able to escape before it fell into the black hole. The fate of the loyalist Cylons who were not on the Colony is likewise unspecified, however, without natural reproduction and with the recovery of resurrection technology impossible, their extinction is a foregone conclusion. Any hope of restoring the resurrection technology was lost when Anders and Foster died: all of the Final Five would have been necessary to rebuild it.