Forty-four years ago the Twelve Colonies and their rebellious creations, the Cylons ended a twelve-year war with an armistice agreement. The Cylons retreated behind a line in space, presumably to found their own homeworld. The agreement led to the construction of the Armistice Station where representatives from the two factions could meet together in peace to discuss possible relations and trade. Every year the Colonials sent a military officer to represent them, and every year the Cylons sent no-one. What was going on behind the Armistice Line was a total mystery. This led to the Colonies maintaining a substantial fleet of more than 120 battlestars in case the Cylons did return with aggressive intent, but beyond that life on the Twelve Colonies slowly returned to normal and the Cylon War eventually just became a memory.
Forty years after the armistice was signed, this changed abruptly. In the interim period the Cylons had developed twelve models that looked completely human and had many thousands, maybe millions, of copies. Many of these humanoid Cylons from seven of the models (knowledge of the other five was restricted among the seven for reasons at that time unknown) infiltrated the Colonies at many levels, mostly in the Fleet and its R&D divisions. One model, known later only as 'Caprica Six', seduced the vain but brilliant computer programmer Dr. Gaius Baltar and helped him develop the Command Navigation Program, which would enable a much higher degree of coordination between spacecraft, both for military and civilian use. Unknown to Baltar, Caprica Six had placed backdoors in the program that would allow Cylon ships to use it to shut down any vessel using it.
The sneak attack was carried out. The Cylons achieved total surprise. Their baseships jumped into the Colonial system and launched nuclear barrages at each of the Twelve Colonies. Thousands of their Raiders launched attacks on Colonial military bases, destroying Colonial Fleet Headquarters on Picon and the Scorpion Fleet Shipyards in the opening minutes of the onslaught. Any Colonial vessel that attempted to respond was simply shut down and destroyed at leisure. There were only two exceptions: the battlestar Pegasus was undergoing a refit at the Scorpion yards and its computer system, including the vulnerable program, was deactivated. Admiral Cain ordered the ship to make a blind hyperlight jump to escape the attack. The battlestar Galactica, the only surviving ship from the First Cylon War, had a standing order that no networked systems were to be used on the ship. Also, the ship was being decommissioned to be turned into a museum to the First Cylon War, and although the CNP was uploaded to the ship there was no need to actually activate it.
Pegasus turned tail and ran from the system, planning to recuperate and launch sneak attacks on Cylon military outposts. Galactica, on the other hand, became entrusted with the lives of just under 50,000 civilians. Laura Roslin, the former Secretary of Education and the highest-surviving member of the government, was named President of the Twelve Colonies and she insisted that Galactica help gather together as many civilian ships caught between the colonies as possible before it also fled the system. Dr. Baltar was among the refugees who managed to find a hiding place in the Fleet. The Cylons seemed to be unaware of Pegasus' survival, but the destruction of Galactica and its fleet (which became known simply as 'The Fleet') became a high priority for them. Their baseships and Raiders hounded Galactica constantly as it fled further into deep space. The Fleet's security was further compromised by the presence of multiple Cylon agents hiding within its population. One of these agents, Leoben Conoy, was exposed and tortured at length. During this torture he revealed that the Cylons now believed in the existence of 'one true God' and had a spiritual frame of reference to justify their genocide of more than fifty billion human beings.
The Fleet's destination was unknown, but its commander, William Adama, decided to perpetuate a lie that he was aware of the location of Earth, the semi-mythical 'thirteenth colony' founded by a splinter group of the Twelve Tribes long before they left the human homeworld, Kobol, for the Colonies. Adama's real plan was to simply keep searching until they found a suitable, habitable planet and set up home there.
Although Baltar had found refuge in the Fleet, he found his position complicated by his guilt over his role in the attack. He chose not to reveal his part in events, and was instead assigned to build a 'Cylon detector' to expose potential Cylon agents in the Fleet. Throughout all of this, he was also constantly having what appeared to be a hallucination of Caprica Six who was egging on his ambition and vanity but also insisting on him accepting the reality of God's existence. Baltar's initial theory that this image was simply a hallucination was discredited when 'Head-Six' provided valuable information leading to the destruction of a Cylon military base, and in time he came to accept that she was a messenger of a higher power.
As the Fleet travelled further into space, its people were unaware that the Cylon devastation of the Colonies was not total. The Cylons had occupied several of the Colonies and were intent on tracking down survivors. A sports team on a training run in the Caprican mountains, led by noted Pyramid star Samuel T. Anders, formed a resistance cell which caused the occupiers a fair amount of trouble through guerrilla warfare. A Raptor pilot from Galactica, Karl Agathaon (callsign 'Helo'), had also ended up abandoned on the planet. The Cylons had failed to develop a method of biological reproduction amongst themselves, despite experimenting on numerous human females to find out what the problem was, and came to believe that the missing ingredient was 'love'. For this reason, a copy of a Cylon infiltrator (a model #8 called 'Sharon Valerii') in the fleet whom Helo had developed feelings for was assigned to help his 'escape'. During this process they fell in love and slept together, and the Eight indeed became pregnant. Unfortunately, the plan worked a bit too successfully, as the Eight rebelled against the other Cylons and aided Helo's escape from the planet.
The Fleet's course led them to Kobol, birthplace of mankind. However, the Cylons had also discovered the planet and left a baseship in orbit to guard it. A Galactica Raptor was shot down over the planet and crash-landed. At the same time, Laura Roslin had started experiencing powerful visions (dismissed by some as a side-effect of the anti-cancer drugs she was taking) which she interpreted as religious in nature. According to the Prophecies of Pythia, the legendary Tomb of Athena on Kobol held within it the key to the location of Earth, but could only be accessed by a relic called the Arrow of Apollo. Roslin convinced Lt. Kara 'Starbuck' Thrace to use a captured Cylon Raider to return to Caprica and recover the Arrow. The loss of a valuable military asset on a fool's errand enraged Adama, and he had Roslin arrested in an apparent coup. Meanwhile, a Raptor infiltration mission successfully sneaked a nuke onto the Cylon baseship and destroyed it, allowing a rescue mission to be launched to Kobol. The Eight infiltrator on Galactica, however, shot Adama twice in the chest before the mission could be launched.
Lt. Kara 'Starbuck' Thrace recovers the Arrow of Apollo from Caprica, though not without resistance.
On Kobol, Baltar's 'Head-Six' led him to the ruins of the Opera House, a grand structure that used to dominate the City of the Gods on the planet, and there he experienced a vision of the Opera House in its fully glory, with a child in a crib inside. According to Head-Six, this child represented an image of things to come.
The Eight was taken into custody and later killed, but Cylon reinforcements arrived and in the resulting battle Galactica was boarded. Colonel Tigh, the ship's XO, successfully repulsed the boarders and the rescue team recovered the missing crew from Kobol. Roslin escaped from custody and led a third of the Fleet back to Kobol, planning to search for the Tomb of Athena. Kara Thrace returned from Caprica, bringing the Arrow, Helo and 'his' Eight with him as well, and they were able to locate the Tomb. A recovered Adama, determined to reunite the Fleet, assisted in this mission and they were able to determine that Earth lay in the rough direction of the Lagoon Nebula. The Fleet, bruised by recent events, resumed its course.
Meanwhile, the battlestar Pegasus had carved a bloody swathe through various Cylon forces as it attempted to escape from Colonial space. During one engagement the ship was boarded thanks to the work of an infiltrator - a Six named Gina - and 800 crewmen were killed. The Cylon was taken into custody and subjected to 'extreme sanction' in an attempt to extract information from it. The Pegasus crew identified a Cylon fleet ahead of them behaving in an erratic manner, which eventually led to them discovering the Galactica and the rest of the Fleet. Initial jubilation quickly turned to distrust: Admiral Cain found Commander Adama's tactics timid and also didn't recognise Roslin's authority as President, whilst Adama learned that Cain had become exceptionally ruthless in her pursuit of revenge against the Cylons, even shooting her XO in the head when he refused an order. Cain authorised her torturers to employ the same tactics on Galactica's captive, pregnant Eight as they had on their own prisoner. Helo and another crewman, deck chief Galen Tyrol, objected to this and in the resulting struggle a Pegasus officer, Lt. Thorne, was killed. Cain had the two men arrested and sentenced them to death. Adama refused to recognise this order and the two battlestars faced off. However, in the face of a threat from the pursuing Cylons, the two sides backed down.
The two battlestars undertook a joint strike mission to destroy a Cylon 'resurrection ship', a relay which allowed Cylon agents killed in the Fleet to download into new bodies in the pursuing Cylon force. The mission was successful, but during the confusion Baltar, encouraged his 'Head-Six', released Gina from her prison on Pegasus. She killed Cain and disappeared into the Fleet. Adama took command of the whole Fleet (helped by a promotion from Roslin to Admiral) and had his men released.
Meanwhile, on Cylon-occupied Caprica both the Six who had seduced Baltar and also the Eight killed on Galactica had resurrected in new bodies. Their experiences among the humans, and their falling in love with humans (Baltar and Galen Tyrol, respectively) had led them to question the wisdom in carrying out the genocide against humanity in the first place. With the knowledge that Helo's Eight was still alive in the Fleet and about to bear their child, the two Cylons proposed a plan for peaceful coexistence with the humans which, they convinced the other Cylons to agree with. When Starbuck led a rescue team from Galactica and Pegasus to recover Anders' resistance group, a Cylon named Cavil accompanied them back to the Fleet and informed Adama and Roslin that the Cylons had declared a unilateral ceasefire, abandoned the pursuit of the Fleet and withdrawn from the Colonies. The Fleet's leaders were sceptical.
Helo and Eight's daughter, Hera, was born. However, Roslin had decreed that the baby in Cylon hands represented a significant threat to the Fleet and had it secretly given over to a human mother to raise, whilst the parents were told she had died from birth complications. Shortly after this Roslin found herself locked in a battle for political survival against Dr. Baltar, whose popularity in the Fleet had reached the levels where he could run against her in the Presidential elections. The discovery of a habitable, terrastial planet within a nearby nebula, shielded from Cylon sensors, became the flashpoint of the election, which Baltar won. He ordered the Fleet to begin the colonisation of 'New Caprica', even after several thousand people were killed when Gina committed suicide by blowing up the Cloud Nine liner with a nuclear bomb.
A year passed and most of the Fleet's population settled on the planet. Although life was harsh and Baltar's administration was not particularly effective, the people at least could grow their own food, breathe fresh air and walk in the open. Then a Cylon reconnaisance ship picked up the EMP from the nuclear explosion from a light-year away. A major Cylon fleet jumped into orbit. The undermanned Galactica and Pegasus (now commanded by Adama's son, Lee) were forced to flee. The Cylons occupied New Caprica, forcing Baltar's government to surrender to them. Still pursuing the agenda laid down by the Six and Eight on Caprica, the Cylons' plan was to see if they could coexist with the humans, but from a position of strength and authority.
For four months the situation deterioated. Human rebels, led by Anders, Colonel Tigh (whose wife Ellen was killed during the occupation), Galen Tyrol and Roslin (helped by her political aide, Tory Foster), kept up a guerrilla war against the Cylons which eventually led to the use of suicide bombers. The Cylons were forced to crack down harder and harder on the rebels, and the situation threatened to spiral out of control. The Galactica launched a rescue mission by jumping directly into New Caprica's atmosphere to launch its fighters to engage the Cylons' air cover, whilst ground forces aided the rebels in evacuating the populace onto the grounded civilian ships. The plan almost went awry when additional Cylon baseships jumped into orbit and inflicted heavy damage on the Galactica, but Pegasus arrived to relieve her. The newer battlestar was destroyed, but took two Cylon baseships with her and kept the pressure up long enough to allow most of the civilians to escape the planet. Two of the exceptions were Baltar, who was imprisoned on one of the Cylon baseships, and Hera, whose identity had been discovered by the Cylons and was being cared for on board.
With Baltar gone, Roslin reassumed the Presidency and the Fleet also resumed its course towards the Lagoon Nebula and, hopefully, Earth. But the scars of New Caprica would not fade easily. More than 5,000 people had died during the whole New Caprica episode, and another 3,000 in the destruction of the Cloud Nine. Several civilian ships had been lost or destroyed on New Caprica, along with the Pegasus, resulting in more people crammed into smaller amounts of space. The supply situation was also becoming increasingly desperate.
Morale was lifted, briefly, by the discovery of a beacon left behind in the Lion's Head Nebula by the Thirteenth Tribe on their way from Kobol to Earth four thousand years earlier, showing that the Fleet was on the right path. Interestingly, around this time Baltar learned on the baseship that the seven extant Cylon models had no knowledge of the 'Final Five' Cylon models beyond the mere fact of their existence. Their names and faces were totally unknown to them, possibly due to programming restrictions. One of the seven models, a Three named D'Anna, started experiencing visions of the Kobol Opera House with five faceless figures located inside, but only in between resurrections. She took to having herself killed again and again so she could download and see more, but there was a limit to what she could remember.
The Fleet's food stores were becoming dangerously low when it came across a borderline-habitable planet circling an unstable sun located in the middle of a dense star cluster. A form of algae grew on this planet which could be transformed into edible food. A major resupply effort was launched and was successful, but towards the end of this process Galen Tyrol discovered a huge, artificial structure in a mountain nearby. According to Pythia's prophecy, this was the 'Temple of the Five', built by the Thirteenth Tribe on its way to Earth. Within the Temple, according to legend, lay an artifact called the Eye of Jupiter which could have revelatory powers. The Cylons arrived and a stand-off ensured between the two forces. The humans failed to locate the Eye of Jupiter and were forced to retreat from the planet as the sun began to go nova. Baltar and D'Anna found the artifact within the temple and D'Anna was blessed with a vision of the Final Five, but immediately died. Baltar was taken prisoner by the last Colonial forces to leave the planet. Resurrected on a Cylon resurrection ship, D'Anna was told by Cavil that her actions had endangered other Cylons and were symptoms of an unhinged mind, as was her obsession with the Final Five. Cavil had her entire line 'boxed', taken offline, to prevent her further contaminating the other Cylon models with her insanity. Meanwhile, Hera was rescued from the baseship by her mother (now referred to by the callsign 'Athena'), aided by Caprica Six, and returned to Galactica to live with her parents. Caprica Six was taken into custody.
After the nova had consumed the system, the Colonials discovered that the nova was mirrored by another the Thirteenth Tribe had seen on their way to Earth, now identified as lying in the Ionian system. Theorising that Earth could be found by following a path from the Algae Planet's system to the Ionian Nebula, the Fleet set out on its new course. Along the way they stopped in orbit over a gas giant to refuel. Captain Kara 'Starbuck' Thrace kept seeing what appeared to be a Cylon Heavy Raider in the clouds, but when she pursued she instead found a yawning storm system which strongly resembled the Eye of Jupiter. Even more disquieting, she realised had been drawing images of the Eye since childhood. Whilst pursuing the Raider into the heart of the storm, she was visited by a 'head-image' of her own, which took the form of the Cylon Leoben, who forced her to relive the experience of her abusive mother's death. Her mother had been convinced that Kara was 'special' but refused to divulge why exactly she thought this. Kara seemed to find a moment of peace just before her Viper was destroyed by the titanic atmospheric pressures at work in the gas giant's atmosphere.
The Fleet approached the Ionian Nebula just as the trial of Baltar was held. Baltar was accused of conspiring with the Cylons during the occupation of New Caprica. Eventually he was cleared, since he was forced to do the Cylons' bidding at gunpoint. During his incarceration Baltar had written out a manifesto showing where he thought the government had gone wrong in its administration of the Fleet, and this had won him some supporters amongst the civilian population, who now gave him shelter. During the final approach of the Fleet to the nebula, four people on board - Galen Tyrol, Saul Tigh, Tory Foster and Sam Anders, now a Viper pilot in training - started hearing fragments of a familiar melody which others apparently couldn't hear. As the Fleet got closer, this music became more familiar and discernable. Eventually, motivated by the song, the four gathered together and were struck by a sudden realisation that they were Cylons, four of the 'Final Five' models.
The Fleet reached the Ionian Nebula and immediately lost all power for several seconds. Just as it resumed four Cylon basestars jumped in on top of them. Forced to remain whilst the civilian ships had to reboot their jump drives from scratch, Galactica engaged the Cylon fleet in a furious engagement. Inexplicably, a Viper appeared from out of the nebula to join the Colonial forces, apparently piloted by Kara Thrace! The Cylons pressed home their superiority of numbers and nearly destroyed the Fleet, but a Raider happened to scan the Viper piloted by Anders and the Cylon force immediately retreated, allowing the Fleet to escape.
The apparently-resurrected Kara claimed to have been to Earth, but her memory of events was hazy. She couldn't remember her Viper exploding in the gas giant's atmosphere, nor could she remember what precisely happened afterwards except her ship appearing above a blue-white planet circled by a single moon and then waking up in the nebula. Despite suspicions over her identity and nature, Adama eventually allowed her to take a civilian ship, the sewage reclamation vessel Dimetrius, and attempt to find her way back to Earth. At this time, Laura Roslin started having visions of the Opera House on Kobol, shared with Athena, Caprica Six and Hera. How this was possible was unclear, although Roslin had accepted a blood transfusion from Hera to retard the progress of her cancer two years previously.
Meanwhile, with the revelation that the Final Five were in the civilian Fleet, the Cylons became divided over what to do next. Cavil (the Ones), the Fours and Fives were adamant it changed nothing and the Fleet should be destroyed as soon as possible. The Twos (Leoben), Sixes and Eights were intent on 'rescuing' the Final Five. To this end they proposed unboxing the Threes and learning more about the Five from her. The two factions split violently, with the result being civil war. One of the Eights rebelled against the rest of her model and joined Cavil. Cavil's forces acheived a surprise victory, almost wiping out the other faction and apparently reducing their forces to a single baseship, which, whilst under heavy fire, made an emergency jump. This crippled baseship was found by the Dimetrius and surrendered to Kara Thrace's forces and was escorted back to the Fleet.
The rebel Cylons and the Colonials agreed to a truce to rescue D'Anna from the Cylon Resurrection Hub, which was the central control node for all Cylon resurrection technology. Destroying the Hub would end Cylon resurrection forever. The rebels were willing to give up their immortality in return for the Colonials' protection and assistance. Adama and Roslin agreed. The assault was a success. D'Anna was recovered and the Hub destroyed. Reluctantly, the four Cylons revealed themselves to the rest of the Fleet and a signal was picked up by Kara Thrace's Viper which led both factions to Earth. The Fleet's jubilation was cut short when they discovered that Earth was a blasted, irradiated wasteland.
Further investigation revealed that Earth had been nuked 2,000 years ago in an intercine conflict between the Thirteenth Tribe and a race of mechanical servitors or proto-Cylons they had created. More shockingly, the Thirteenth Tribe themselves were revealed to have been humanoid Cylon models analogous to the modern seven 'skinjobs', although they were more sophisticated and able to bear children. The four Cylons experienced flashbacks indicating they had lived on Earth two thousand years ago and had been killed in the nuclear war, but it was unclear how or when they resurrected or got to the Colonies. During one vision, Saul Tigh was with his wife Ellen on Earth, indicating that she was the fifth and final Cylon. With Ellen killed during the New Caprica occupation, this knowledge seemed of limited value.
Shock and despair spread through the Fleet. Several crewmembers committed suicide, and even the Cylons were affected, with D'Anna choosing to kill herself by abandoning herself on the ruins of Earth. Despair turned to anger, and some among the Colonials turned their blame on their new Cylon allies, refusing to allow them to join the Fleet or gain representation in the government. When Roslin and Adama decided to not only press on with this process, but to also install Cylon technology in all ships of the Fleet to improve their performance, the result was an open mutiny. Almost a hundred civilian and military personnel were killed (and the Cylon Anders was badly wounded) before Adama and Roslin reasserted control of the Fleet. The Fleet's goal after this time was straightforward: to find a new hospitable planet, any planet, and settle on it. The mission achieved a new urgency when it was discovered that all of the damage Galactica had sustained over the last four years was in danger of bringing about a total structural failure of the vessel.
Meanwhile, Ellen Tigh had not died on New Caprica, but had been resurrected on a Cylon baseship commanded by Cavil. Her memories restored, Ellen recalled how the Final Five survivors of the Thirteenth Tribe had rebuilt the resurrection technology originally developed on Kobol but lost after they had developed natural procreation. The Five had travelled to the Colonies on a sublight ship (taking 2,000 years to reach them, although due to relativity only a few years had passed on board) and ended the war between Colonials and Cylons they found in progress when they arrived. They offered to help the Cylons build humanoid models to help them better emulate their God, but the first model, Cavil, rebelled against the Five's plans to peacefully integrate Cylon and human, blanked their memories and exiled them to live amongst the humans. Cavil then unleashed the nuclear holocaust against the Twelve Colonies out of a desire for vengeance.
With the help of a sympathetic Eight, Ellen escaped back to the Fleet, but this turned out to be a ruse so the Eight could kidnap Hera and return her to Cavil. With the Resurrection Hub destroyed, Cavil wanted to dissect Hera to learn how the Cylons could biologically reproduce themselves. Cavil based his efforts at the Colony, the massive Cylon space station which was their effective homeworld. The Fleet was unable to locate the Colony, since Cavil had it moved shortly before the civil war had begun. This became of more pressing importance when Kara Thrace discovered that a drawing done by Hera was actually a musical score, that of the same song which had 'activated' the four Cylons in the Ionian Nebula and also a song that Kara's father had taught her when she was young. Hera seemed to know or be connected to whatever 'higher power' had engineered Kara's resurrection and led the Fleet, indirectly, to Earth.
The rebel Cylons, in an effort to help heal the critically-wounded Anders, had plugged him into their datastream. Anders was somehow able to determine the location of the Colony: located on the accretion disk of a naked singularity. With Galactica dying, Adama decided to send the ship out in a blaze of glory rather than letting her fall apart in open space. With both the recovery of Hera and the opportunity to totally destroy the Colony and Cavil's faction for good at stake, Adama and his crew began to plan their final assault...
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