The series leads us to believe that the Galactica and it is fleet are all that survived the destruction of the Colonies, but is that true? with only two hundred and twenty ships, not all survivors might have had the chance to get onboard, and indeed, are we really sure that the First Fleet (which contained the last five Battlestars) was really the only remnants of the Colonial Fleet? May not other ships have survived and just were in another place at the time of the ambush?
In which case, with other ships out there, what will they do?
Some may have heard of the Galactica's travels and decided to either try and team up with her, or gone their own way. They may or may not have civilian ships accompanying them, and they may or may not have Cylons on their heels, but the chances of that are almost 100 percent.
While the extermination of the Colonies will be complete at some time, who, when they believe the job is not yet done, is just going to stand around and watch? This game takes the form of a small Colonial force against huge numbers of Cylons. The Colonials will start with surprise, and will almost always be fighting with fanatical zeal, but in the end this will be a guerrilla warfare game. Although if the Colonials somehow win, then the Colonies may be rebuilt at some future point, and then who knows, a large fleet may be sent to follow the trail of the Galactica itself, armed with start of the art new and modern weapons and ships.
Or of course, the other option is that the Colonial fleet just launch into a final battle with the Cylons. The Colonials have nothing now to live for, so they would be out for blood, which would suit the Cylons fine as it would mean that they would not have to track down the fleet.