This episode appears to be based upon a successful WWII operation based upon the 28th suggestion from the "Trout Memo" written by Rear Admiral John Godfrey and his assistant, Lieutenant Commander Ian Fleming, who you might recognize as the author of the James Bond books.
Operation Mincemeat, part of the wider "Operation Barclay", this was basically a means of planting misinformation to be swallowed whole by the Nazi high command. I cannot give details without spoiling the episode, so watch it. I can only say, it worked beautifully.
Operation Naye'i, or "Operation alien gods" as referred to in this episode, is a fictional World War II operation based upon operation mincemeat... but it was basically the same thing. This episode dresses it up similarly to the way the X-Files does in the episode "Anasazi", with native American mythology and characters. The best stories are the one based on a kernel of truth, and that was done here, making this one of the most profound episodes of Space Above and Beyond.
What is interesting with this episode is that it also refers to the use of "telepresence" otherwise known as "Waldos", which was an idea created by Robert Heinlein about controlling machinery remotely using computers... something that we have done with the Mars Rovers. So the events of this episode are not too far-fetched. Cooper Hawks was concerned that a person operating a spaceship using telepresence would not be able to participate in a dogfight scenario believably because they would not actually be there in the "big hairy furball". He actually assists the person operating the telepresence with occasional insight during the mission.
Captain Vansen however was miffed because her squad's spaceships had been futzed with without her knowledge and unknown technology inserted. As she tells the Admiral, she does not want to be privy to classified information but she does want to be notified when she and her squad would be called upon to be put into danger.
This is one of the first missions where Shane Vansen acts as captain, after being elevated to that position.
