Founded on August 2, 1947 as a response to the reported UFO crash landing at Roswell, Bureau 39 was a covert branch of the military that is dedicated to protecting America from alien threats. Bureau 39 showed up to the Kent farm in Smallville in 1966, the day after the ship carrying an infant crash-landed on the outskirts of town. Despite the best efforts of farmer Jonathan Kent to bury the ship, Bureau 39 found and confiscated it.
Bureau 39 continued to operate in secret for decades, eventually catching wind of the first appearance of Superman in Metropolis. Using phony warrants, under the leadership of Jason Trask, they interrogated reporters Lois Lane and Clark Kent for information. After Lane and Kent gained access into Bureau 39's base, they were used as live bait in the Bureau's unsuccessful attempt at killing Superman. After this incident Bureau 39 went rogue and began operating on it's own agenda.
After Bureau 39 was dismantled and Jason Trask killed a great number of their files were acquired by Intergang, these files were then used to verify that the Red Kryptonite that they had found contained all the properties of regular Green Kryptonite but affected Superman differently.
- Bureau 39 is shown to have had some connection to this reality's Project Blue Book, which is a reference to the real-life study of UFOs by the United States Air Force.
- Bureau 39 is shown to have extensive files and info spanning decades, including files on well know UFO sightings in Roswell, New Mexico and Gulf Breeze, Florida.