Battle of the Colony
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Plans for the battle begin in earnest shortly after the child Hera Agathon is kidnapped by a Number Eight, Sharon "Boomer" Valerii, and taken to the Colony for experimentation (TRS: "Islanded in a Stream of Stars"). Initially, Admiral William Adama did not want to entertain such a prospect, as Galactica was under repair, and in no shape to fight. However, Adama comes to have a change of heart, and secretly seeks the assistance of Samuel Anders in locating where Valerii could have taken the child. Weighing his options, he gathers his crew on the hangar deck, asking for volunteers. Enough of them agree to join him for Galactica itself to go into the fight, and not just a small Raptor assault team.
A Raptor scout, crewed by Lieutenant Margaret "Racetrack" Edmondson, and Lieutenant Hamish "Skulls" McCall, seeks out the location of the Colony, finding it buried in a field of stellar debris orbiting a naked singularity. This complicates matters, as it leaves Galactica only one location to jump to - point blank range in front of the Colony's gun batteries (TRS: "Daybreak, Part I").
The Cylons also enlist volunteers, including several dozen freed Centurions, painted with large, red stripes across their torsos to distinguish them from the otherwise similar Centurions on board the Colony. Confident in his plan, Admiral Adama authorizes the mission. Before setting off, he hands over control of the fleet to Junior Lieutenant Louis Hoshi who is remaining behind on the Rebel Cylon baseship, while Romo Lampkin is sworn in as President of the Colonies, in place of Lee Adama and Laura Roslin, who both volunteer for the mission.
The baseship formally takes over CAP duties as Galactica jumps away.
The battle begins as Galactica jumps within range of the Colony. The Cylons detect Galactica, and open fire. The ship takes a beating from both large and small calibre batteries, causing the ship to violently rock in every direction, but Galactica's hull holds together. Anders, now connected to Galactica's systems via the CIC, connects to the Colony's Hybrids, and orders them shut down. Recognizing his signature, the Hybrids comply, and the Colony's weapons cease functioning. This causes the Colony to launch its massive Raider compliment.
With the Colony's weapons offline, Galactica launches its remaining Vipers, while at least fifteen Raptors jump directly from the starboard flight pod in a flanking position to board the Colony. The stresses involved in jumping directly from the pod result in structural failure, leading to explosive decompression of the entire pod, and the destruction of any remaining museum pieces.
After the planes are away, Admiral Adama orders flank speed, ramming the battlestar's dense "alligator-head" bow into the Colony, punching a large hole in the Colony's side. Rappelling down from four airlocks, Lee Adama leads a strike team of volunteers and "Red Stripe" Centurions, while Raptor strike forces led by Capt. Kara "Starbuck" Thrace, Capt. Karl "Helo" Agathon, and Jr. Lt. Sharon "Athena" Agathon cut their way in elsewhere on the Colony's hull, however, not all Raptors survive the flight. Pilots "Cartwheel", Lt. Edmondson, and Lt. McCall are known to have been killed after their respective Raptors are struck by debris from the dense stellar cluster. Before being struck, Lt. Edmondson, and Lt. McCall arm their nuclear payload assuring themselves they're not flying in cold.
Inside the Colony, both strike forces push onwards despite opposition from not only modern Centurions, but older Model 0005 Centurions. Capt. Thrace's team is the first to discover Sharon "Boomer" Valerii, 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. As the rest of the team retreats back the path they came, Sharon "Boomer" Valerii is gunned down by Sharon Agathon, in retaliation for taking her daughter. They are able to reconnect with Lee Adama's strike team before retreating back to Galactica.
During this time, John Cavil goes on the offensive, taking a Number Four and a Number Five, as well as a team of Centurions and boards Galactica, making his way to the CIC. Hit and run firefights break out all over the ship, as marines and Centurions duck in and out of various corridors, with both sides suffering heavy casualties. Dr. Gaius Baltar and Caprica Six are among the many that help defend the ship, and are able to take down Centurions that prevent Lee Adama and Lt. Thrace from advancing further. Both parties begin making their way back to the heavily defended CIC, after Hera is taken away by her parents. Along their way, they are ambushed by a Number Five, who guns down a marine, and hits Capt. Karl Agathon in the leg, before being killed by Capt. Thrace. While Sharon Agathon and others work to close Capt. Agathon's wound, Hera runs off and disappears. Laura Roslin, working in sickbay, senses Hera's return and chases after her, 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 and take Hera with them to CIC, recreating their movement as seen in their visions, encountering the Final Five there, standing on the CIC balcony.
Upon entering the CIC, they discover that the loyal Cylon forces have broken through, but are ultimately killed by officers inside, while Cavil is captured by a marine. In the process of being removed from the CIC, Galactica is rocked by another massive hit, and Cavils takes the opportunity to overpower his captor, and quickly takes Hera hostage. Mocking the Colonials' situation, Cavil demands to be let go, and wants to take Hera with him, stating she is the best hope for his kind after the permanent destruction of Cylon resurrection (TRS: "The Hub"). Baltar successfully talks Cavil into a truce in exchange for Hera's life. Colonel Saul Tigh sweetens the pot by offering resurrection in exchange for a permanent truce between humanity and the Cylons. Cavil agrees, and calls off his forces, while the Five collectively work to rebuild the ancient organic memory transfer technology. Galactica recalls its Vipers, ultimately losing four in the battle, with a fifth on fire as it lands in the port flight pod.
The truce is short lived, as the Five work to rebuild Cylon resurrection, their memories become linked, and all are able to see into each other's lives, including Tory Foster's memories of murdering Cally Tyrol by flushing her out of an airlock (TRS: "The Ties That Bind"). The remaining four are shocked by what they see, with Galen eventually breaking the link, and snapping Tory's neck in a fit of rage. Her death destroys any chance of Cavil regaining resurrection, which causes the loyalist Cylons in the CIC to open fire on the officers inside. The firefight is short lived, as Number Four, and Number Five are quickly killed, and Cavil commits suicide by placing his gun to his mouth. Outside of the ship, Cylon Raiders resume their attack on Galactica. The ship is left undefended, and takes more damage.
At this moment, debris strikes the Raptor belonging to Lt. Edmondson, and Lt. McCall, still adrift in space, causing Edmondson's stiff hand to fall on the launch mechanism for the onboard nuclear payload. The missiles launch towards the Colony, and detonate, immediately lighting the Colony on fire, and knocking it out of orbit, causing it to begin falling towards the singularity, taking Galactica with it. Both vessels are struck by debris, as Admiral Adama calls upon Capt. Thrace to activate the ship's FTL drive, and jump the ship back to the Fleet, but she unable, as she does not have the Fleet's rendezvous coordinates. Just as Adama calls for a blind jump, she realizes that the mysterious music played by her father, and given to her by Hera Agathon, forms FTL jump coordinates. As visions fill her head, she enters the coordinates and activates Galactica's FTL engine. As the Colony continues to fall into the singularity, Galactica jumps away, leaving it to its fate.
The toll of battle and its structural frailty are too much for the old battlestar. As it completes the jump, Galactica suffers a series of critical structural failures, causing its lateral structural members to collapse, and permanently destroying its FTL jumping capabilities. The ship is rocked by a series of explosive decompressions as its members collapse, throwing officers, and crew around inside, while Vipers and Landrams are tossed from the flight pod. After the ship settles, its sublight engines re-engage, as the ship drifts over a dull, greyish moon, orbiting a habitable planet ahead. Twelve hours after the battle, the civilian fleet, along with its basestar escort, rejoins Galactica in orbit of the planet. The Colonials, along with the surviving Twos, Sixes, and Eights, will eventually move to settle the planet, while the baseship is given to the freed "Red Stripe" Centurions. This marks the end of the Colonial's four year exodus from the Colonies after the Cylons attacked, and a permanent end to Colonial/Cylon hostilities.
Those who settle did not learn whether any of the Cylons on the Colony were able to escape before it fell into the black hole. However, without natural reproduction and with the recovery of resurrection technology impossible, their extinction is a foregone conclusion. All of the Final Five would have been necessary to rebuild it, so any hope of restoring resurrection was lost when Anders and Foster died (TRS: "Daybreak, Part II").