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More than fifty-eight years before the destruction of the Twelve Worlds, the humans of the Colonies created the Cylons, a race of sentient machines whose history and destiny were forever tied to their human "parents".
According to the Sacred Scrolls, man lived alongside the Gods in the birthplace place of humanity: the planet Kobol. In truth, humanity lived alongside its creation, the Cylons, who, over time, evolved into humanoid form. Though these humanoid Cylons were indistinguishable from their human creators, they were unable to procreate, instead relying on organic memory transfer to download their consciousness into new bodies after death (TRS: Miniseries, "Kobol's Last Gleaming", "Revelations", "Sometimes a Great Notion", "No Exit").
Though in the ancient texts, Kobol was described as paradise, war and human sacrifice -- either figurative or literal -- plagued the planet. Humanity and the Cylons also came into conflict, forcing the humanoid Cylons to flee Kobol and travel to the distant planet Earth where they settled (TRS: "Valley of Darkness", "No Exit").
Two thousand years later, the human inhabitants of Kobol abandoned their world and journeyed to the Twelve Worlds, where the Twelve Tribes settled colonies. Over time the memory of what happened on Kobol faded, passing into cryptic legends portrayed in the Colonials' Sacred Scrolls, which referred to the Cylons only as a "Thirteenth Tribe" (TRS: Miniseries, "Kobol's Last Gleaming", "Revelations", "Sometimes a Great Notion", "No Exit").
On Earth, the Thirteenth Tribe prospered, building a new civilization and a modern age of technology. Moving beyond their original limitations, the Cylons of Earth were finally able to reproduce and memory transfer and resurrection technology were abandoned and forgotten. As civilization on Earth continued to grow, a new race of mechanical Cylons were created, ancient versions of the Cylon Centurions (TRS: "Sometimes a Great Notion", "No Exit").
Roughly two thousand years after the colonization of the Thirteenth Colony, Earth's mechanical Cylons rose up. A devastating war ensued and Earth's inhabitants were wiped out in a nuclear holocaust (TRS: "Revelations", "Sometimes a Great Notion").
Five survived the holocaust -- Samuel Anders, Tory Foster, Saul and Ellen Tigh, and Galen Tyrol - later coming to be called the Final Five. These survivors were researchers involved in the rediscovery of resurrection technology -- a technology from Kobol which allowed individuals to be reborn (or downloaded) after death in duplicate bodies. Having anticipated the attack, the Final Five resurrected aboard a ship waiting for them in orbit of Earth (TRS: "Sometimes a Great Notion", "No Exit").
Fearing their human cousins in the distant Twelve Worlds would suffer the same fate as the humanoid Cylons of Earth, the Final Five departed in their vessel, beginning an approximately 2,000-year-long sublight journey in order to prevent such a catastrophe (TRS: "No Exit").
First Cylons in the Twelve Colonies
The first Cylons in the Twelve Colonies were created (or recreated) by Doctor Daniel Graystone, a brilliant computer scientist and CEO of Graystone Industries on the colony of Caprica. Known as the U-87 Cyber Combat Unit, or Cybernetic Lifeform Node, the prototypical Cylon was created as cannon fodder for the Caprican Military. Though its design called only for soldiers capable of "shooting and fighting", the U-87 achieved true sentience through the integration of the robotic body with the meta-cognitive processor, a device stolen from Graystone competitor Tomas Vergis of Tauron. The mega-cognitive processor, or MCP, was a revolutionary new artificial brain that - though it never worked for Vergis - served as higher intelligence for the U-87 once uploaded with the living virtual avatar of Daniel Graystone's recently deceased daughter, Zoe Graystone (CAP: "Pilot", "The Imperfections of Memory", "Unvanquished").
A New Race
Though Graystone thought that his attempt at resurrecting his daughter by implanting her personality into the U-87 was unsuccessful, Zoe Graystone lived on as the first fully sentient Cylon consciousness. Unable to reproduce the MCP with the Zoe avatar driving it, Graystone Industries scientists struggled to meet the Caprican Military's order for 100,000 battle-ready units. Finally, however, the avatar was removed from the chip when the U-87 prototype was destroyed. Rebooting the original chip from the ruined chassis, Graystone Industries was finally able to duplicate the MCP for mass production (CAP: "Ghosts in the Machine", "End of Line", "Unvanquished").
Seeing beyond their application as robot soldiers, Daniel Graystone spoke of the potential of Cylons as a new race that would walk alongside man:
Delivering the first line of U-87s to the Caprican Military, Graystone scientists were unaware that remnants of the Zoe avatar still existed on the MCP, making the U-87s recognize and even obey people from Zoe Graystone's past. With the Tauron crime syndicate, the Ha'la'tha, controlling Graystone Industries in tandem with Daniel Graystone, a black market was created for Cylons, with the robots being shipped to the colonies of Gemenon and Tauron without the knowledge or consent of the Caprican Government (CAP: "Unvanquished", "False Labor", "Blowback").
The Differently Sentient
As the threat by the monotheist terror group, the Soldiers of the One, culminated in the attempted bombing of Atlas Arena in Caprica City, a turning point was achieved. Using a squadron of Cylons to target and kill a group of STO terrorists at Atlas, Daniel Graystone prevented the bombing and the deaths of 100,000 Capricans. The event at the arena galvanized the public in support of Cylons as protectors of the Twelve Worlds, with statues erected in their honor. Within five years of the U-87's development, several new lines of Cylons were created to serve various functions in Colonial society (CAP: "Apotheosis").
Cylons quickly became integrated into life on the Colonies, with Cylon servants and Cylon workers becoming a common sight on the streets of worlds like Caprica. With that integration came questions about Cylon sentience, notably addressed by Sister Clarice Willow, former STO leader and monotheist cleric, who lead congregations of Cylons - communicating through the virtual world - in worship of a singular, all knowing, all powerful God:
The First "Skin Job"
While Cylons were becoming commonplace in the Colonies, the Zoe Graystone avatar - having survived the destruction of the original U-87 chassis - lived exclusively in the virtual world. Though she attended Clarice Willow's Cylon sermons, the Zoe avatar was primarily concerned with the construction of a new robotic body that would allow her to exist in the physical world (CAP: "Apotheosis").
Working with her parents, Daniel and Amanda Graystone, Zoe labored to create a body more suited to her. Utilizing Daniel Graystone's expertise in robotics and Amanda Graystone's experience as a plastic surgeon, the family was successful in building the first "skin job": a mechanical skeletal structure with human-looking skin and hair. The body was activated in the Graystones' private lab - a perfect, robotic copy of their daughter and the true rebirth of Zoe Graystone into the physical world (CAP: "Apotheosis").
The Cylon War
...And then the day came when the Cylons decided to kill their masters. Within just a few years of their introduction, the Cylons revolted, resulting in a costly and protracted war known as the Cylon War. Humanity responded by unifying their once fractured coalition of worlds into a federal republic, with each of the Twelve Worlds signing the Articles of Colonization. A stipulation of the articles was the construction of battlestars to defend each of the Twelve Worlds, supplemented by other military craft including the Viper fighter and the workhorse, multifunction craft called the Raptor (TRS: Miniseries, "Razor").
Man Versus Machine
Cylon Centurions - derisively referred to as chrome "toasters" by the Colonials - were the mainstay warriors in the battle against their human oppressors, with various models serving in a variety of roles and functions. Though humanity was unaware at the time, the Centurions were deeply religious, a trait passed down to them by U-87 model inhabited by the monotheist Zoe Graystone. The Centurions operated basestars (vessels comparable to the Colonial battlestars) and fighter vehicles known as Raiders (comparable to Vipers and Raptors). The Centurions also utilized computer viruses to infiltrate Colonial computer networks, undermine defenses and disable vessels (CAP: "The Heavens Will Rise", "Here Be Dragons", TRS: "Fragged", "No Exit").
The Cylon War was fought on the surface of the Twelve Worlds as well as on outlying planets and in space. During an operation late in the war, rookie Viper pilot Ensign William Adama crashed his plane on a remote ice planet, stumbling upon a Cylon installation. Inside the installation, Adama discovered evidence of a bizarre experiment in which the Cylons used human captives to perform dissections. The result of those experiments was the creation of the First Hybrid, an evolutionary "dead end" in the Cylons' attempt at creating their own flesh and blood bodies. As the war came to a close, that Hybrid escaped aboard a basehip with a handful to Centurions - later passing into Cylon legend as The Guardians (TRS: "Razor").
The casualties mounted as the war stretched on for twelve and a half years. Ultimately, the Final Five arrived at the Colonies and met in secret with the mechanical Cylon race. Promising to aid the Cylons in creating humanoid bodies, the Final Five brokered an end to the war and departed to create a new world. With an armistice declared and the war over, the Colonials were left to rebuild their worlds, abandoning much of their advanced technology - including holobands and computer networks - for fear of future Cylon attacks (CAP: "Pilot", TRS: "Razor", "No Exit").
In their exile, the Cylons worked with the Final Five to build a Colony and perfect their mechanical form. They also labored to upgrade their baseships and raiders, and continued the development of the Hybrids. The Cylons also developed their humanoid form, creating thirteen organic models - though nearly perfectly human were unable to biologically reproduce like their ancestors. Living alongside both Cylon War-era Centurions, the new humanoid Cylons feared their own mechanical uprising and developed new Cenurions, implanting them with telencephalic inhibitors that repressed self-awareness and higher brain function (TRS: "Exodus, Part I", "Six of One", "No Exit").
The first of these organic models was John Cavil, also known as Number One, who was patterned and named after Ellen Tigh's father. Cavil assisted in the development of the other seven models, but became jealous of the attention Ellen paid to Daniel, the seventh humanoid Cylon. Contaminating the amniotic fluid in which the Number Seven copies were being grown, Cavil corrupted the model's genetic formula, destroying the entire line. Consumed with jealousy and bitterness over the limitations of life as an organic being, Cavil became obsessed with vengeance against the Final Five. Capturing and boxing the Final Five, Cavil planted them on several of the Twelve Colonies and provided them with false memories and new identities. Cavil also reprogrammed his humanoid Cylon kin, preventing them from thinking about or discussing the Final Five (TRS: "No Exit", "The Plan").
Planning and Provocation
As the Five lived unaware of their true identities on the Colonies, the Colonials themselves, having had no contact with the Cylons in decades, began to take provocative steps. Six years before the Fall of the Colonies, the Colonial Fleet dispatched the battlestar Valkyrie on a reconnaissance mission, deploying a stealth fighter across the Armistice Line and into Cylon territory. Though the stealth vessel was only briefly in their space, the Cylons acted swiftly, destroying the fighter and capturing the pilot, Lieutenant Daniel Novacek (TRS: "Hero").
Though the Valkyrie's intelligence mission was a failure, the Colonial Fleet commanders' suspicions were correct - the Cylons were preparing a war machine. Using humanoid models as agents, the Cylons planted operatives in key positions in the Twelve Worlds, working from the inside to undermine Colonial defenses. Among those Cylons deployed to the Colonies, a Six - later called Caprica Six - was placed in a key position to sabotage the Colonial Defense Mainframe by seducing (and falling in love with) its designer, Doctor Gaius Baltar. Agents were also planted in the Colonial Fleet, including another Six, Gina Inviere aboard the battlestar Pegasus and an Eight, Sharon Valerii aboard the Galactica. A Two was also highly placed within the Colonial Government (TRS: Miniseries, "Downloaded", "Pegasus" "Resurrection Ship, Part I", "Razor", "The Plan").
Though their worship of a single, all powerful God provided the Cylons with a moral direction, many - though not all - believed the extermination of the human race was justifiable. While some models viewed the attack on the Colonies as a preemptive strike against an aggressive adversary, others viewed it in more philosophical terms, believing that parents have to die for their children to grow (TRS: "Bastille Day", "Downloaded", "Lay Down Your Burdens, Part II", "The Plan").
Humanity's Children Return Home
More than forty years after their disappearance, the Cylons returned to the Twelve Colonies in force. Surrounding the Colonies with fleets of baseships, the Cylons unleashed a torrent of nuclear missiles and waves of raiders equipped with computer viruses capable of infiltrating and disabling Colonial ships' operating system software (TRS: Miniseries, "Razor", "The Plan").
As the bombs fell on the Colonies, and cities like Caprica City were wiped from existence, the personal vendetta of John Cavil took shape. Having planted his "parents", the Final Five into Colonial life, Cavil took particular satisfaction in watching them suffer through the annihilation of the human race. Forcing them to experience the destruction of the Colonies, however, was not enough for Cavil, who pulled Ellen Tigh from the wreckage and placed her on an escaping ship to later be hunted by the Cylons. Miraculously, all of the Final Five survived the destruction of the Twelve Worlds, four of them escaping into space, the fifth, Samuel Anders surviving in the mountains of Caprica (TRS: "Tigh Me Up, Tigh Me Down", "The Resistance", "No Exit", "The Plan").
With the total destruction of the Scorpion Fleet Shipyards and scores of battlestars, many Colonial vessels attempted retreat, but only a handful survived the assault. The plan received mixed reviews from its Cylon engineers with models including Threes considering a success beyond their expectations, while others, like "Tough Six" and John Cavil considering it a failure. Still the Colonial Fleet was destroyed and the Colonies themselves subjected to nuclear bombardment - humanity was all but wiped out, save a handful of survivors on the ground and in rag-tag fleets of escaping ships (TRS: Miniseries, "Downloaded", "Razor", "The Plan").
Believing that any survivors allowed to escape would return to seek vengeance on them, the Cylons pursued the remnants of humanity. Chasing a fleet of ships led by the battlestar Galactica well beyond explored space, the Cylons dogged the survivors, making several attempts at destroying them. Nevertheless, the fleet continued, under the command of Cylon War veteran Commander (later Admiral) William Adama and surviving Colonial cabinet member, later President Laura Roslin (TRS: Miniseries, "Exodus, Part II").
In the devastated Colonies, the Cylons slaughtered most of the survivors they were able to capture, though some were taken to "farms" where they were subjected to medical testing and experiments: an attempt at solving the persistent reproductive problems of the Cylons by trying to fertilize human women with Cylon DNA. Though the farms proved unsuccessful, the Cylons remained on the Colonies, hunting survivors and fighting a resistance movement led by Samuel Anders - unaware of his true nature as one of the Final Five. They also worked to repair the damage they had done, removing bodies and repairing structures and replanting trees, the Cylons occupied the Twelve Worlds, taking them for their own (TRS: "The Resistance", "The Farm", "Downloaded").
Cylon Occupied Caprica
An extension of their attempt at creating a human/Cylon hybrid, the Cylons deliberately allowed a single survivor - Lieutenant Karl Agathon, a Raptor pilot - to remain alive, wandering the woods and abandoned cities of Caprica with his former shipmate, Sharon Valerii. In reality, Agathon's companion was another Cylon agent, an Eight sent to fall in love with him and conceive a child. As Agathon and Valerii ostensibly evaded capture as they searched for a way off the planet, the two were forced into intimacy and ultimately conceived a child. The experiment, however successful, backfired on the Cylons when Valerii - apparently truly in love - began helping Agathon in earnest to avoid capture while keeping her true nature secret (TRS: "33", "Six Degrees of Separation", "The Hand of God", "Colonial Day").
Pursuit of the Fleet
With agents embedded in the escaping vessels and a tracking device planted aboard the battlestar Galactica, the Cylons attempted to bring the fleet down from within while simultaneously attacking it outright. Still, despite the Cylons' efforts, suicide bombers, sabotage and months of interstellar battles proved unsuccessful in eliminating the human fleet. Though their identities were still unknown, the existence and presence of humanoid Cylons quickly became common knowledge, further damaging the Cylons' advantage. Still, the four members of the Final Five residing in the fleet remained unaware of their true identities, Saul Tigh even acting as first officer of the Galactica alongside its commander, Cylon War veteran William Adama (TRS: "33", "Water", "Litmus", "Crossroads, Part II").
Cylons Versus Galactica
Within its first few months on the run, the fleet led by the Galactica was engaged by the Cylons in battle numerous times. The first conflict occurred as the Galactica armed itself and gathered its fleet to leave the Colonial star system at Ragnar Anchorage. Having discovered the Cylons' attempt at sabotaging the battlestar's CNP program, the crew of Galatica and Gaius Baltar - having survived the holocaust - purged the mainframe computer removing that particular Cylon advantage. Deploying a squadron of antique Viper Mark IIs from Galactica's Cylon War museum, the Colonials engaged Cylon basestars and raiders, providing the fleet cover in order to jump to safety. With the Cylons successfully repelled, the Galactica itself jumped away, leading the fleet to a new home - the mythical planet described by Colonial Sacred Scrolls, Earth (TRS: Miniseries).
The Cylons quickly regrouped and pursued the Colonial fleet. As the Cylon fleet tracked the Galactica and its fleet jump after jump, a group of Cylon agents - John Cavil, Aaron Doral, Leoben Conoy, and Shelly Godfrey - worked from inside to disrupt, sabotage and destroy the fleet. Another Cylon - an Eight posing as Raptor pilot Sharon "Boomer" Valerii - was planted aboard Galactica as a sleeper agent, acting against her ship under hypnotic suggestion. Cut off from the rest of their fleet, these Cylon agents bungled attempt after attempt to destroy the fleet, only able to contact the others after being killed and resurrected aboard a nearby Resurrection Ship (TRS: "33", "Water", "Litmus", "Six Degrees of Separation", "The Plan").
Further undermining the Cylon agents' attempts to destroy the fleet, were their own "human" failings. Like the Number Six, Shelly Godfrey who fell in love with Gaius Baltar after trying to frame him for treason, a Four calling himself Simon O'Neill likewise fell in love with and married a human. Having spent years as an agent in the Colonial Fleet, O'Neill later refused orders to sabotage the a vessel in the rag-tag fleet, choosing to commit suicide rather than betray his human wife and adopted daughter (TRS: "The Plan").
Galactica Scores a Victory
After being on the run for weeks, the Colonial fleet was in desperate need of refueling. Discovering a rich source of tylium ore on an asteroid occupied by the Cylons, Commander Adama determined to take the fuel by force. Marking the first offensive against the Cylons, the Colonials planned an operation involving decoy ships to draw the Cylons' attention away from the asteroid as a squadron of Vipers led by Captain Lee Adama attacked the Cylon tylium processing plant. Though the operation proved costly in terms of equipment and manpower, the Colonials prevailed, sending the Cylons into retreat. As Commander Adama described it: "If you keep running from the school yard bully, he keeps on chasing you but the moment you turn around and stop you punch him really hard in a sensitive spot. He'll think twice about coming back" (TRS: "The Hand of God").
Believing they possessed a greater knowledge of human religion than the Colonials did themselves, the Cylons traveled to the planet Kobol where Colonials believed life originated. Placing a basestar in orbit, the Cylons laid in wait, hoping to catch the Fleet seeking refuge. Soon, the Colonial fleet detected Kobol and dispatched a scout of three Raptors to survey the planet. Destroying one of the Raptors immediately, the Cylons forced another to jump back to Galactica while the third crashed on Kobol. On Kobol the survivors fought for survival against a landing party of Cylon Centurions, engaging them in multiple firefights (TRS: "Kobol's Last Gleaming, Parts I & II", "Scattered", "Fragged").
With the Cylons waiting in orbit, the Colonials were unable to rescue their men, choosing instead to send a Raptor piloted by Sharon Valerii - still unaware of her true nature - to plant an explosive aboard the basestar. Using a Cylon tracking device to disguise her ship as a captured vessel, Valerii and her co-pilot Margaret Edmondson flew their Raptor inside the baseship and planted a nuclear device. As she attempted to arm the nuke aboard the baseship, Valerii was confronted by a group of Eights, who allowed Sharon to plant the bomb and depart before the device detonated, destroying the Cylon vessel (TRS: "Kobol's Last Gleaming, Part II").
Returning to the Galactica victorious, Valerii's Cylon programming activated and she shot Commander Adama twice in the chest, point-blank range. With the Galactica in chaos, another Cylon basestar attacked the fleet, forcing the Colonials to abandon Kobol and retreat. However, in the confusion, the fleet was separated from the Galactica, leaving it vulnerable to attack (TRS: "Kobol's Last Gleaming, Part II", "Scattered").
Fearing for the safety of the civilians at jump coordinates unkown, Colonel Saul Tigh took command of the Galactica jumping the ship back to its original coordinates and back to the Cylons in order to locate the fleet. Fighting off a Cylon barrage, the coordinates were discovered and the Galactica jumped away once again, but not before taking on a boarding party of Centurions. Using the same tactics they employed during the Cylon War, the Centurions disabled Galactica and overran the ship, attempting to reach its atmospheric controls and vent the crew into space. Despite losing a handful of officers to brutal hand-to-hand combat with the Centurions, the crew of Galactica prevailed, repelling the Cylon boarding party, repairing the ship, and returning to the Fleet. In addition, the Colonials also acquired the Cylon party's ship, a Heavy Raider, allowing them study and cannibalize its technology (TRS: "Scattered", "Fragged").
With their fleet reunited and its commander on the mend, the Colonials continued their flight to Earth - and the Cylons tracking them. Unknown to the humans, however, another Colonial vessel, the battlestar Pegasus had also survived. Conducting hit-and-run operations against Cylon installations including a communication relay and Raider staging ground, the Pegasus tracked the Cylon fleet only to discover its target: the Galactica. Joining with the Galactica, the presence of the Pegasus gave the Colonials further advantage and resulted in yet another offensive against the Cylons (TRS: "Pegasus", "Resurrection Ship, Parts I & II", "Razor").
Locating and targeting the Cylon Resurrection Ship - a previously unknown vehicle - the Colonials planned an operation to take it out, thus temporarily robbing the Cylons of their ability to download into new bodies. The combined offensive action resulted in the destruction of an entire fleet of basestars and the ultimate destruction of the Resurrection Ship, sending the Cylons into retreat (TRS: "Resurrection Ship, Parts I & II").
Though the Colonials were victorious, the Cylons scored their own victory when a captured Cylon agent, Gina Inviere, escaped her cell aboard Pegasus and assassinated the ship's commander, Admiral Helena Cain. Though other commanders rose to take Cain's place, the command structure aboard Pegasus was weakened - a fact demonstrated when the ship's new commander was killed when the Cylons lured Pegasus into an easy ambush (TRS: "Resurrection Ship, Part II", "Captain's Hand").
Still, the Cylons became cautious, changing their tactics to reflect their loss of resurrection. Even Raiders - which were capable of downloading after being destroyed - behaved differently, choosing not to engage Colonial fighters in battle, but rather lure them into traps. Though the loss of the Resurrection Ship created yet another disadvantage for the Cylons, the loss was only momentary and a new ship was soon placed into service (TRS: "Scar", "The Plan").
A New Plan
Having failed time and again to destroy the more than fifty-thousand survivors aboard the Colonial fleet, and continuing to suffer attacks from the human resistance movement on Caprica, the Cylons' plans changed (TRS: "Lay Down Your Burdens, Part II", "The Plan").
Heroes of the Cylon
After being killed aboard the Galactica in retribution for shooting - though not fatally shooting - William Adama, Sharon Valerii was resurrected and sent to live on Cylon occupied Caprica. There she was heralded as a hero, but struggled to cope with life as a former sleeper agent, unable to move beyond her life aboard Galactica. Taking up residence in her old apartment in Delphi, Valerii - continuing to go by her Galactica call sign "Boomer" - proved a threat to the Cylons who valued unity and conformity in their culture (TRS: "Resistance", "Downloaded").
Also struggling to reconcile her actions as an undercover agent, Caprica Six - haunted by a vision of Gaius Baltar - was sent to meet Boomer in order to help her move on. Though Six was unaware of it at the time, she too proved a threat to Cylon conformity and was sent to meet with Boomer in order to prevent both from being punitively boxed. This however backfired and together the "Heroes of the Cylon" worked to change the course of action pursued by their people. Influenced by their love and affection for humanity - Six for her love of Baltar and Boomer her love of Galen Tyrol - the Heroes convinced the Cylon majority that the genocide and occupation of the Colonies was immoral. With this vast change in philosophy, the Cylons abandoned the Colonies, allowing a One to be captured and taken aboard Galactica where he informed humanity that it could return home (TRS: "Downloaded", "Lay Down Your Burdens, Part II", "The Plan").
Following a rescue mission to retrieve survivors from Caprica - including Samuel Anders and his resistance group - the fleet led by Galactica continued its search for Earth, refusing the offer from the Cylons to return to the now abandoned Colonies. As Colonial society became split over the prospect of settling on a planet dubbed New Caprica, the Cylon agent from Pegasus, Gina Inviere detonated a nuclear device in orbit of the planet - a signal to the Cylons of the fleet's location (TRS: "Lay Down Your Burdens, Part II").
Ultimately choosing to settle on New Caprica, the Colonials abandoned most of their fleet for a makeshift village on the planet's surface, leaving the Galactica and Pegasus to patrol in orbit. Despite the patrols, however, the planet was protected by a nebula that masked its presence from the Cylons for more than a year. Detecting traces of the nuclear detonation, the Cylons eventually discovered the planet and surrounded it. With the Colonials caught totally by surprise and the Galactica and Pegasus in retreat, the Cylons were offered the unconditional surrender of humanity (TRS: "Lay Down Your Burdens, Part II").
Though the Cylons were ostensibly there for peaceful coexistence and cooperation with humanity, the situation on New Caprica quickly devolved into an occupation. While this new course for Cylon/human relations - spearheaded by Caprica Six and Boomer - was far more peaceful than their previous attempts at genocide, the Cylons nevertheless resorted to brute force, restricting many freedoms and leading to a resistance movement. As the Cylons battled the resistance, the Galactica and Pegasus regrouped and returned to rescue the colonists. With both ships engaged in heavy combat with the Cylons, the Pegasus was destroyed, taking out several basestars in the process. Themselves complacently underpowered in terms of reinforcements, the Cylon occupiers fled New Caprica, taking Gaius Baltar and the half-human, half-Cylon child Hera with them (TRS: "Exodus, Parts I & II").
The Race to Earth
The Cylons abandoned New Caprica as well, retrieving the Cylon-hybrid baby from the planet by happenstance, and turned their attention to the same objective as the Colonials: finding Earth. Using the research of Gaius Baltar (who resided with the Cylon fleet at the time), the Cylons located the Lion's Head Nebula. A scouting basestar found an ancient beacon in the area, verifying that the Thirteenth Tribe did pass through the area on their way to Earth. But the Cylon scout ship met with disaster; the probe was contaminated with a pathogen that, while benign to humans, infects, deactivates or kills all Cylons, their ships, and their entities (Torn).
The Cylon fleet, which also includes a second Resurrection Ship, abandoned the scouts and cut off further communication, believing that the virus could replicate through their resurrection process. The Cylon scout ship eventually self-destructed and the Cylons managed to prevent the infection from spreading, although, unknown to the Cylons, the Colonials gained a critical biological warfare option (A Measure of Salvation).
The Number Three units exhibited strange behavior in attempting to ascertain the identities of the Final Five Cylon models, as they had seen in visions prior to a model being resurrected. At the algae planet, while the Cylon majority attempted to gain information on the location of Earth by way of the Eye of Jupiter, the Threes' ulterior motive to seek knowledge of the Final Five disturbed the collective status quo and command consensus of the Cylon majority to the point where all Three models were boxed for their aberrant behavior (Rapture)
The Final Five
Unknown to either the Cylon or Colonial commanders and leaders, four Colonials exhibited strange behavior that ultimately brought them to come to the discovery that they are Cylons. Saul Tigh, Galen Tyrol, Samuel Anders and Tory Foster were the only crewmembers that could hear a strange melody that drew them to meet each other in a room on Galactica, shortly after the Fleet arrived at the Ionian nebula. The nature of these particular Cylon models, especially given Saul Tigh's existence as a decorated veteran of the Cylon War, was unclear and likely fundamentally different from other humanoid Cylons.
During the ensuing battle, one Raider identified Anders as a Cylon, which caused all Raiders to break off the battle and forced the Cylon fleet to retreat. Because of this, a Number One decided to lobotomize the Raiders to prevent such insubordination in the future. This decision was opposed by a faction, led by Natalie, who advocated the search for the Final Five and who desired to unbox Number Three to learn what she found at the Temple of Five. The disagreement between these factions led to a violent conflict between the humanoid models. This eventually leads to the Battle of the Resurrection Hub where resurrection is destroyed by a combined attack force from the Rebel Cylons and the Colonials. Eventually the Rebel Cylons and the Colonials destroy the main enemy Cylon faction in the Battle of the Colony. The remainder of the Rebel Cylons settle on the new Earth with the Colonials while they let their Centurions have the Rebel Basestar and their freedom to find their own destiny.
The Parent Trap
In the Re-imagined Series, an Oedipus theme exists between the creations (Cylons) turning on their creators (Colonials). The humanoid Cylons themselves draw the analogy of children murdering their parents:
Oedipus is the tragic character of Sophocles' play Oedipus Rex. Without realizing it until much later, Oedipus murdered his father Laius and married his mother Jocasta, with whom he had several children, just as the Cylons had tried to do in the farms.
All the Significant Seven models view each other as "siblings".
Cylon Evolution Tree