The cylons planned and then encroached on the 12 colonies infiltrating them from within to shut down their defense grids, their capital ships and their air superiority. They destroyed everything they could find and then nuked it all from orbit. Their goal was to exterminate the humans from the universe for their destructive tendencies. However to their dismay, two of the colonial Battlestars (ships of the line) managed to escape the assault on the colonies. The Battlestar Galactica and the Battlestar Pegasus.
The Battlestar Galactica escaped the extermination along with approximately 70 other ships leaving for a total of 50,000 human survivors. Realizing that the way against the cylons had been lost long before it even started, Commander Adama, the commanding officer of the Battlestar Galactica changed his focus from hunting down the cylons in a futile chase to protecting what was left of the human race, the 70 ships in his fleet. A woman with terminal breast cancer named Laura Rosalin (the former Secretary of Education) was deemed the new president of the 12 colonies. Through an experimental treatment for her cancer, she led the civilian fleet back to Kobol where they found a star map leading them to earth.
The Battlestar Pegasus also escaped. Being the last battlestar to escape the supply yards orbiting one of the 12 colonies, it also ran into a civilian fleet not unlike the one that the Galactica ran into. The Commanding officer of the Pegasus, Admiral Kane, decided to commandeer any useful personnel and supplies from the civilian ships and throw the rest to the dogs for the crusade to glory against the Cylons. After a year and a half of cat and mouse games the Pegasus accidentally stumbled upon the Galactica. However the two mindsets that the two warships had adopted in the year and a half of running for their life was polar opposite.
This disagreement stemmed from the most fundamental definition of what it meant to be human now with 50,000 survivors left in the galaxy. Gaius Baltar, the main responsible for the Cylons breaking through the colonial defenses released an imprisoned model six cylon on the Pegasus and armed it. Soon after it's release, it Murdered Admiral Kane and was taken into hiding by Gaius. Following those events, Pegasus had two temporary replacements, Commander Adama was promoted to Admiral, and his son, Lee "Apollo" Adama, was promoted to Commander of the Pegasus.
Another half a year passed by and finally the humans found a new home to rest their heads. A barely habitable planet they dubbed New Caprica in commemoration of the crown jewel of the 12 colonies that was subsequently the first colony to be hit when the cylon nukes fell. There was a large amount of disagreement over whether or not the fleet should colonize New Caprica which was only resolved after Gaius Baltar was elected president during the bi-yearly elections. However, the day before the fleet was ordered to settle onto New Caprica by the new President Gaius Baltar, the six he had released from custody on the pegasus detonated a nuke which he had supplied her with for sex which acted as a beacon for the Cylons who had long since lost the scent of the Galactica.
The civilians spend a year and a half in a Stalag-like internment camp under the Cylon control. The Galactica and the Pegasus has jumped out when they saw five Cylon flagships jump in (flying skeleton crews and knowing it was a suicide mission to even attack now). However after a year and a half, Admiral Adama and Commander Adama formulated a plan to rescue the colonists on New Caprica. The mission ended in the loss of the Pegasus after abandon ship of all hands was issued and the Humans continued to survive in thinned numbers.
Back on the road, supplies were beginning to wear thin, primarily, food. Several weeks were spent trying to find a planet with any form of edible vegetation which eventually came in the form of a planet which was rich in algae. During the collection operations for the Algae, the Deck Chief for the Galactica stumbled up a temple called the Temple of the Five. This caused another encounter with the Cylons as a specific cylon model 3 who called herself DeAnne, needed to know who the final five (or the five survivors of Earth) were. After her Discovery of the faces of the final five, the system's star went nova forcing all parties to vacate the system. DeAnne died by a brain aneurysm and when she resurected, the cylon model Ones put her entire clone line into mothballs.
The Deck Chief, however, picked up on some clues he remembered from the days when his father, a pastor, used to tell him about the chamber of the five, and pointed out a nebula which the next clue to earth was supposed to be. A nebula. Along the way, Kara Thrace, a hot-shot degenerate viper pilot, saw a vision of earth which caused her to dive straight into the eye of a gas storm on a gas giant, causing her viper to explode.
Arriving at the nebula 2 months later, however, they were greeted by two Cylon Flagships and Kara Thrace. This was to everyone's dismay. No one could explain how she had arisen from the dead or how she managed to find them after 2 months worth of jumps. It was at this moment that the 4 of the Final five (the fifth being dead) began hearing a song that allowed them to realize that they were the final five. But all the other pieces to their puzzle were still missing at this point.
The Cylon Fighters, now realizing that the final five were among the human fleet refused to engage them any longer and as such the nebula was finished. Kara Thrace, however was their roadmark to earth. This fact was contested by everyone in the fleet being long set in their ways of "trust no one that just spontaneously appears." Admiral Adama, not wanting to discount any means of finding earth again, gave Kara Thrace a ship and a skeleton crew to go search for Earth on their own. It wasn't until the final hour before they were bingo fuel, that a Cylon heavy raider (their transport ships) showed up with shocking news. A Cylon civil war had broken loose.