I've installed the fleet operations and extracted the dominion wars mod but when I load the fleetops exe from dominion wars and try to load a map, it says insert CD. Not sure what else I need to do or I have missed a step.
You need to either have an Armada 2 CD or a GOG.com executable file to play Fleet Ops, otherwise you could play it without ever buying the base game (Armada 2). If you own the GOG version of Armada 2 ($10 on GOG.com) you need to copy the file "Armada2.exe" from that game, rename it to "Armada2.ldl" and place that in the \Data folder of your Fleet Ops installation.