The DOE runs all of the US' National Laboratories...the labs (and the DOE itself) have an intelligence and counterintelligence operation, as well.
ETA: the DOE's origins are in the Manhattan Project, then the Atomic Energy Commission. The Atomic Energy Act of 1946 established the National Laboratories under the purview of the AEC, which eventually turned into the DOE. The DOE's roots are in defense and it is still intertwined with the DOD for many things, not least of which as the "owners" of our nuclear stockpile. No department in the federal government has more expertise (real expertise, not talking head expertise) in science and research than the DOE.
ETA: the DOE's origins are in the Manhattan Project, then the Atomic Energy Commission. The Atomic Energy Act of 1946 established the National Laboratories under the purview of the AEC, which eventually turned into the DOE. The DOE's roots are in defense and it is still intertwined with the DOD for many things, not least of which as the "owners" of our nuclear stockpile. No department in the federal government has more expertise (real expertise, not talking head expertise) in science and research than the DOE.