Sorry for a long answer, I recently found out how to play Star Trek Armada 2 after much searching and thought I'd tell people encase they were finding it difficult.
[First] download the iso here:
http://isohunt.com/torrent_details/112873445/Star+Trek+Armada?tab=summary or have the original disk.
[Secondly] After download is completed mount the disk to a virtual drive, or burn the disk and place in tray.
[Thirdly] Download Star Trek Armada 2: Fleet Operations and install, found here:
http://www.fleetops.net/home.html
[Fourthly] Patch Fleet Operations to version 3.2.6 with both updates... version 3.2.3 first. These are found here: http://www.fleetops.net/download/Download/FleetOperations3.0/
[Fiftly] Download the mod called 'A2 Classic' found here:
http://www.moddb.com/games/star-trek-armada-ii/downloads/a2-classic and unpack the rar into the directory of Fleet Operations in the file that says mods.
---This is done by right clicking the desktop icon, click 'Open file location' or finding it in programs, now once open, double click the 'Data' file and the mod file will be contained inside. Unpack the zip file inside.
[Lastly] Launch Fleet Operations and go to options in main menu, you will see mods as an option, click and you can launch Star trek Armada 2.
This now allows you to play the original game on the Fleet Operations tweaked engine and is compatible with all newer operating systems. I rally hope this was helpful. thanks.