Their religion was based around Cloister, who was frozen in time to save the holy mother and her children, and that he would one day return to lead her children to Fushal, the promised land. (actually reflecting Dave's ambition to open a farm on Fiji). A war was waged over this religion, the origins of which are sketchy.
The Cat race was all but destroyed during the war, and what few that remained left Red Dwarf. Only the Cat himself remained on the ship by the time Dave Lister woke up. Most of the Cats attempted to leave Red Dwarf aboard two White Giants, with the two factions of Felis Sapiens taking individual White Giants. One faction immidietly crashed into an asteroid upon leaving the mothership, and the other was lost to the dark blackness of space. Whether or not they survived it uncertain.