What is the plot and theme of Battlestar Galactica?

Originally written as an answer for a question on Quora.

There are those who believe that life here began out there. Far across the universe. With tribes of humans, who may have been the forefathers of the Egyptians, or the Mayans. Who may have been the architects of the Great Pyramids, or the lost civilization of Atlantis. There are those who believe there may yet be brothers of man, who even now fight to survive, somewhere beyond the heavens.

The backstory of Battlestar Galactica begins millions of years ago, on a world called Kobol, located somewhere on the other side of the universe. Kobol was the home world of the humans, a race made up of thirteen tribes each ruled over by a Lord - The Lords of Kobol. They were an advanced race of architects and scientists, builders of great pyramids and temples. At some point in their history the thirteen tribes left Kobol, although it is not made clear in the series whether this was through choice or to escape some disaster. Twelve of the tribes chose to stay together, and set off in one direction, while the thirteenth set off on their own. They were never heard from again, although there were rumours that they founded their own colony on the far side of the universe. The remaining twelve colonies travelled for a short time before they found a star system with enough worlds on which to settle. Each colony took it's own home world, naming it after a sign of the zodiac, but came together in establishing a federal style of government. They lived peacefully for many millions of years, befriending races in neighbouring star systems.

Not far from the system of the Twelve Colonies was a world that had once been home to an alien race of intelligent reptilians. These reptilians, known as the Cylons, had built themselves a collection of robotic servants. Over time the reptilian species had died out, but their race of machines lived on, gained sentience, and continued to be known as Cylons. These Cylons were intensely xenophobic and distrustful of organic lifeforms. They had generally left the colonies alone, but had begun to wage war on a neighbouring system that were also allies with the Twelve Colonies. When the Colonials intervened to defend their friends, the Cylons adopted a new policy. The total extermination of the human race.

When the Battlestar Galactica series begins, the Colonies have been at war with the Cylons for a undetermined number of years. Possibly centuries. The governor of one of the Colonies, Baltar, has been in discussions with the Cylons, and has somehow managed to get them to agree to peace talks. He has arranged a peace summit with the ruling council, The Council of the Twelve, at a location some distance from the Colonial home worlds, and under escort by the entire Battlestar fleet. The president, the council, and the commander's of all but one of the Battlestars are confident that these talks will lead to a lasting peace with the Cylons. Commander Adama, of the Battlestar Galactica, is not so sure. Unlike his fellow commanders, he continues to launch regular fighter patrols. During one such patrol, a squadron of Galactica fighters discovers a battalion of Cylon ships, hiding in a cloud and waiting to attack. The peace summit is a trap, orchestrated by the Cylons with the aid of Baltar. With all the Battlestars at the summit, the colonies are completely undefended and are wiped out by a massive Cylon force while their military is distracted.

Following the massacre, only a single Battlestar, the Galactica, remains. Commander Adama sends out a message to the survivors to set sail in any ship that will carry them. Together, the last survivors of humanity set out on a quest in search of the thirteenth tribe and the world they are rumoured to have settled on. Earth.

The mission of the Cylons throughout the series is inconsistent. The emperor, known as the Imperious Leader, who ordered the annihilation of mankind also orders the execution of Baltar. Even though he aided them in the attack he is human, and it is the mission of the Cylons to exterminate all humans. There are no exceptions. The Cylon Centurion guarding Baltar draws a dagger, ready to carry out the order, but the Imperious Leader stops him, stating that he wishes Baltar to be returned to their home world for public execution. The prisoner is led away. The Imperious Leader's ship is then destroyed in battle at the end of the episode. His successor sends for Baltar, and informs him that he intends to spare the human's life. He states that he intends to be less extreme than his predecessor, and that he wishes Baltar to go after the escaping humans with a message of peace. He spared Baltar, he will spare them. He also gives Baltar a Basestar, entirely under the human's command. What is inconsistent is that, as soon as Baltar catches up with the fleet, before any kind of communication is made, the Cylon's launch an attack. There is no attempt to issue a message of peace or truce. The Cylons appear to be back to their original mission to completely exterminate the human race. If this is the case, why is Baltar spared? Why is he made, not only a commander, but a senior commander? (He has authority over all bases and outposts his ship encounters.) He is, after all, human. It is hinted, in a short speech from Commander Adama at the end of each serial, that the difference between the current Imperious Leader and his predecessor may actually be that he intends to honour the original agreement made with Baltar. To allow the survivors to live, under Baltar's subjugation. However, this is never clearly stated in the series.

Fleeing from Cylon tyranny, the last Battlestar, Galatica, leads a rag tag fugitive fleet on a lonely quest. A shining planet known as Earth.