The war with the Cylons started when the Colonials received a distress call from their alien allies - the peace loving Hasaris - who were under attack from a race known as the Cylons.
It is not known why the Cylons attacked the Hasaris, but a generally held belief is that the Cylons percieved them as a threat of some kind, either as to Cylon expansion, or as a race that would attempt to curb Cylon intentions. Either way, the Cylons decided that they couldn't be allowed to exist, and thus in typical fashion decided to remove them - permantently.
This started out by the Cylons simply attacking civilian ships and lone warships in a pirate style series of raids, but then when the Hasaris started defending their convoys and ships, the Cylons sent in Baseships with the edict of extermination. The Hasaris tried to defend themselves as best they could, but they were simply no match for the size of the Baseships and the sheer numbers of Raiders that the Cylons could throw at them.
The Colonials sent aid, in the form of a large battle fleet, to help defend the Hasaris from the robotic invaders, and were horrified to learn first hand of the brutality of the Cylon fleet and their ships capabilties. Whilst it was clear from the start, that even flying outmoded equipment, Colonial pilots were superior to their Cylon counterparts, the Cylons could employ far greater numbers than the Colonials could even dream off. And skill alone couldn't fend off the Cylon fleet.
In the span of two yahrens, the Colonial Fleet, and the Hasaris race, were destroyed. Humans could outfly Cylon Raiders in any battle, but they would never be able to match sheer numbers, nor the destructive power of the Cylon Baseships.
Because of this intervention, the Cylons learned about Humanity, and felt that it too, constituted a major threat to their well being and their order of the Universe, and thus had to be removed. There could be no chance for peace or negotiation. Only the complete extermination of the Human race would satisfy the Cylons. Exactly what had happened to the Hasaris.
The Cylons moved on the Colony worlds, and the war began in earnest.
The war went badly for the Colonials. Not having learnt as much of the Cylons as the Cylons had of the Colonials, they were unprepared for the all out nature of the Cylon assaults. As the Cylons wanted the Colonials exterminated, prisioners were not taken, unless the Cylons needed information, and then the prisioners were teminated afterwards. Outposts were destroyed, civilians butchered without mercy.
The Colonial Fleet was not up to the task of stopping the Cylon might completely. While Colonial pilots fought bravely - and always outnumbered - there were simply too many Cylons, and the early ships of the line were not up to the task of taking on the Cylon Baseships.
However one thing that the Cylons hadn't counted on, was the human tenacity and refusal to bow out and allow themselves to be killed. This meant that Cylon advances were never as great as they should have been, and the Colonials hung on, something the Cylons could never understand.
However the Cylons were stopped. In their arrogance, they couldn't believe that the Colonials could stop them - maybe slow them, but not stop, and they launched an all out invasion of the Colony Worlds. The Colonials had not only anticipated this attack, they stopped it dead and had the Cylons running.
The middle stages saw the most action and the least conquest. The Colonials had some initial breathing space as the Cylons decided how to react to the humans recklessness and backed off to mere probing attacks instead of all out assaults.
Another reason for the Cylons pulling back, was that the Colonial destruction was not the sole plan of the Cylons. They had an Empire to forge out, a galaxy to explore, other races to contact, and be ordered into the Cylon Empire or enslave or destroy. The Cylons did venture out far into the galaxy, further out then the Colonials ever imagined or did themselves, but it is not known just how far they went or how many races they contacted. They did ally themselves to some races, and it has never been made clear what constitutes a threat to Cylon Order.
It is due to this that the entire Cylon fleet was never actually employed against the Colonials, which was a good thing, as the Colonials would never have stood a chance.
The Colonials however, put this breathing space to good use. They overhauled their fleet, firstly building the new light cruisers to escort the ageing Heavy Carriers and other ships of the line, before retiring them when the Battlestars entered service. Other ship types soon followed, as did the Viper fighter.
Despite the fact that the Colonials were now on a war footing, one of the first Battlestars produced - the Atlantis was sent out on a mission to try and locate the Thirteenth Tribe. After a while of regular communications, the Atlantis ceased sending and its whereabouts are unknown, even to this day.
It is interesting to note that while these designs were updated and modified over the course of their long service history, the Colonials preferred to overhaul old ships rather than design new ones, and hence the amount of ship designs over the 1,045 yahrens of the war was pitifully small.
With these new ship designs, and a better understanding of how the Cylons waged war, the Colonials conducted their own attacks, and finally brought the war back to the Cylons.
While the Cylons could never actually be driven back, neither could they advance, and the Middle stages of the war was one of probing assaults, strikes and counter strikes into each others terrorities, but very little actual conquest.
The current permanent combat footing and way of life for the Colonials was developed here. During this period, there were many lulls in the fighting, and these lulls sometimes lasted tens of yahrens. To civilians growing up in this era, these lulls were often misinterpreted as seperate wars of their own.
During this time, the Colonials never forgot their neighbours. When the Cylons attempted to attack allied planets, the Colonials always tried to help. Sometimes this worked and they freed their allies from the oppression of Cylon rule, and sometimes they lost.
Inevitably, the Cylons had had enough. Destroying a race was never meant to be slow and tedious a process, and so they put their collective heads together to destroy the humans. They had an Empire for real, and the Colonials were a thorn in their side to be removed for good.
Thus they started learning from their enemies, and became sneaky and treacherous, employing any sort of ambush and bait to trap and destroy the Colonials. It is in this fashion that they got their reputation for being underhand. Any trick to bait Colonials - distress calls, hostage bait, trojan horse traps - all were deemed acceptable if the end result was the death of more Colonials.
One thing that never changed though, was that their tactics always involved overwhelming odds and enough firepower to make sure that the Colonials were destroyed. Sometimes it worked, sometimes it did not. The end result though, was always a drain on ever shrinking Colonial resources.
All the decisive battles of the war were played out in this stage of the war, and while the Colonials managed to inflict major damage on the Cylons (nearly always destroying more than they lost, even in their defeats), they were generally on the defensive just trying to stem the relentess advances of the Cylons.
Despite this extra offensive state of the Cylons, no one suspected that the end was nigh and that the endgame was finally being played out.
How the Cylons got to Baltar, one of the Council of Twelve is still unclear, but they managed to corrupt him, or play on the darker side of his nature, and he in turn managed to convince President Adar that the Cylons wanted Peace. The destruction of the last Colonial Fleet (The Fifth Fleet) was ironically the last straw to Adar who then seemed convinced the Cylons wanted peace (after all, they were just protecting themselves from Colonial intrusion claimed Baltar, and remember, the Colonials did start the war by helping the Harsis). The main Colonial Fleet consisted of just 5 Battlestars at this stage (some lighter elements were available for patrolling and anti-piracy actions, but the last capital ship (generally anything bigger than a Destroyer) was destroyed with the gamble of the Fifth Fleet) and these were led to the moon of Cimtar where the Cylons played their hand and destroyed the fleet and the homeworlds in one move. Only one Battlestar survived, and with the destruction of the Colonies, it escaped into deep space.
The War is generally considered over at the this point, although the destruction of the Human race was not accomplished.