The aliens are here again, at least in terms of popular culture, if not fact. The hottest topic among U.F.O. enthusiasts is what they describe as the Federal Government's experience with aliens, especially the ''Roswell Incident.'' U.F.O. researchers cite a newly discovered document, dated Nov. 18, 1952. It discusses a secret Federal team known as Majestic-12, or MJ-12, established by President Truman on Sept. 24, 1947 to investgate the of the spacecraft and its crew. The document purportedly recounts a secret briefing to President-elect Eisenhower by Rear Adm. Roscoe H. Hillenkoetter, the first director of the Central Intelligence Agency. According to the document, Admiral Hillenkoetter was a member of Majestic-12. ''It appears to be genuine,'' said William L. Moore, who wrote a book about the incident and who investigated the document for more than two years after a colleague received it anonymously in the mail. ''On 07 July, 1947,'' it says, ''a secret operation was begun to assure recovery of the wreckage of this object for scientific study. Aerial reconnaissance discovered that four small human-like beings had apparently ejected from the craft at some point before it exploded. These had fallen to earth about two miles east of the wreckage site. All four were dead and badly decomposed due to action by predators and exposure to the elements.'' Stanton T. Friedman, an nuclear physicist in Frederickton, New Brunswick, Canada, said ''We're dealing with something of extraordinary importance.'' Dr. Maccabee, the Navy physicist, conceeded that skeptics often made valid points. ''[Yet] over the past 40 years there have been 100,000 sightings, with 10 to 20 percent that are hard to explain.'' In the case of the purposed Eisenhower documents, he said, ''maybe somebody's been clever, but I think there's a good chance they are authentic.''