Stick to historical references and mythology.
Shivan names are generally best if from the darker aspects of Hinduism and the Abhrahamaic traditions a little Zoroastraisim helps too.
For the Vasudans Egyptian mythology.
For the Terrans Greek, Roman, Norse and historical places/names/events work best. The more obscure the better and more ironically tied to the mission the better.
The "SD Xenu" "SD Cthulhu" and "SD Sauron" are not good examples of names. (I cringe every time Lovecraft or Tolkein is used, and black out whenever things like 'Voldemort' or 'Vader' are used as its even worse) Nor is randomly tossing together letters to make something that 'sounds good.'
Pick things that add depth to the missions and add another side to them. Something that seems straightforward can be made sinister by names referencing to something similar but different enough.