Fleet Command's latest official version (3.3) can be found here:http://www.moddb.com/mods/freespace-fleet-command-v3
It requires Homeworld 2 v1.1. After patching the game to v1.1, extract the .big file found in the mod's download to the Homeworld 2 Data folder. Then, create a shortcut to the game's executable. In the "Target" line, add these bolded entries to the end:
\Bin\Release\Homeworld2.exe" -mod FSFCv3.big -w1920 -h1080
Where the numbers past W and H are your screen's resolution values.
Launch the game using that shortcut you just modified, and enjoy!