The Reimagined Series (2003)
During the First Cylon War, the mechanical Cylons and Humans fought to a draw. An armistice was signed and the two sides drew a border between Colonial (Human) space and Cylon space. The Cylons withdrew into their own territory to form their own society, and generally avoided any contact with Humans for the next four decades. At the edge of Human space, an Armistice Station was built to allow Humans and Cylons to meet for diplomatic relations. Each year the Humans sent an officer; the Cylons sent no one—until 40 years after the war ended, when the Cylons suddenly reappeared at Armistice Station with no warning. But now they no longer resembled machines; instead they looked exactly like ordinary Humans. The Cylons destroyed the Armistice Station, thus beginning their final assault on the Twelve Colonies and Humanity.
After destroying the Armistice Station, the Cylons launched a sneak attack against the entire Colonial fleet. Taking advantage of their immense knowledge of advanced technology, the Cylons exploited a backdoor in the Colonial military's software written into Dr. Gaius Baltar's programs by Number Six, a Cylon working undercover who had become Baltar's lover, and who deliberately used him to find weaknesses in the Colonial defense systems he had designed.
Using the knowledge they had gained from the unwitting Baltar, the Cylons were able to override the sophisticated computer systems on each battlestar and viper fighter in the fleet and shut them down, thus rendering the ships defenseless. Within a few hours virtually the entire Colonial fleet had been destroyed. Despite President Adar's "unconditional surrender" of the Twelve Colonies, the Cylons did not respond, and detonated nuclear bombs on each of the planets. Casualties were extreme, and within a few hours, over 50 billion humans were dead. Within 24 hours after their initial attack, only the battlestars Galactica and Pegasus had survived, although they would not learn of each other's existence for some time. The Cylons, sometime after, occupied the Twelve Colonies. The nuclear attack did irreversible damage to the planets themselves: the nukes spread out so much radiation and did so much damage that the planets were going to go into nuclear winter according to Gaius Baltar. Caprica was shown to be clearly changing just days after the attack, and any survivors needed a supply of anti-radiation medication. The once blue-green world's sky turned noticeably orange, with the trees and vegetation slowly dying from radiation. Even though the Cylons ultimately abandoned the Colonies, the humans couldn't return to their homeworlds, as they were now devastated nuclear wastelands and were now uninhabitable for a very long time (as of the present day, some 150,000 years and counting).
The Plan shows exactly what happened: after preparing a massive fleet at The Colony (Cylon base that was basically the Cylon home world and site of the final battle between Galactica and the Cylons), the Cylons jumped their fleet into the orbits of the Twelve Colonies. Three battlestars in orbit of Caprica detected them, but one of the Hybrids hacked into the Defense Mainframe using the CNP backdoor and shut it down so the people on the ground couldn't detect them and defend against them. Raiders used the CNP weakness to disable the battlestars in orbit and their fighters and then launched massive pods containing multiple (at least a dozen) nuclear missiles each at each of the Colonies. Once the pods reached a certain height, they broke open and the nuclear missiles spread out and struck their various targets, nuking the Colonies. The Cavils hoped that the Final Five would have learned their lesson about humanity, be killed in the nuclear destruction and download into new bodies on board a Resurrection Ship, but each survived the attack with Cavil even helping Ellen out as he felt she hadn't learned her lesson and needed to live among humans for longer to learn it.
Battle of Ragnar
Following the destruction of Admiral Nagala's flagship, the Battlestar Atlantia, Commander William Adama of the Battlestar Galactica ordered the remnants of the fleet to regroup at Ragnar Anchorage for a counterattack; however, with nearly the entire Colonial military fleet destroyed, it was a civilian convoy led by newly-sworn-in Colonial President Laura Roslin that responded to the orders. Facing limited options, Commander Adama chose to have the Galactica defend the convoy while each ship jumped into deep space, away from the destroyed colonies. The Galactica managed to hold off two Cylon basestars as ship after ship executed faster-than-light jumps to a safe location. When the civilian ships had jumped, the Galactica then joined them. Nevertheless, less than 50,000 Humans - out of 50 billion - had survived the holocaust. Galactica and its fleet of refugees would later find that they were not the sole survivors. At least one other battlestar, the aforementioned Pegasus, had also escaped destruction. Lt. Karl "Helo" Agathon and Lt. Kara "Starbuck" Thrace would also learn that some humans had managed to survive the Cylon attack on Caprica. While this implies that at least some humans left behind by Galactica may have survived the Cylon attack and occupation of the Twelve Colonies, it is unknown if any did.
After the fight at Ragnar, the fleet jumped past the Red Line and into uncharted space to find a new home. Unknown to the new Fleet, they ended up with thirteen Cylons within it: the Final Five, the Cavil responsible for the destruction of the Colonies and the war that followed, two Sixes, a Doral, a Leoben, a Three, a Simon and a Sharon who was a sleeper agent on Galactica. A year later, the human fleet would link up with another survivor of the attack, the Battlestar Pegasus. Eventually the survivors discovered a habitable planet they named New Caprica and were able to settle on it for a year before being invaded by the Cylons and captured. The fleet was able to escape but not without thousands of casualties and the loss of Battlestar Pegasus under command of Commander Lee Adama.
According to Saul Tigh in Battlestar Galactica: The Resistance, twenty billion people died in the attack of the Twelve Colonies; in "A Disquiet Follows My Soul", both Kara Thrace and Felix Gaeta put the number at fifty billion.
After five years of searching, the Colonials found a new world and named it Earth. Just before Earth was found, Galactica faced the Cylons in a final climactic battle and destroyed them forever. All that were left was a group of rebel Cylons that had allied with the human fleet and settled with them, while its surviving, remnant mechanical counterparts, having finally been freed by the humans and rebel Cylons to "find their own destiny", would eventually leave the galaxy in peace, never to return.