once you have put out enough units to bring the flag ship out, just save up resourses or by full artillery if you have not allready. when the flag ship shows up bring it in range and buy a carrier and some battleships, while hitting it with artillery. it's pretty easy.
 "The Peacekeeper"){kind=icon}
 "Mars Colonies Demo"){kind=icon}
 "Colony"){kind=icon}
 "Black Navy War"){kind=icon}