I know the episode you're thinking of. It starred Robert Duvall as a kind of deep cover specialist, undercover ops and all that. Aliens landed and a determination was made that the only way that the proper authorities could learn the intentions of these extraterrestials and prepare for them was to do extensive genetic engineering on Duvall's character to make him into one of those beings.
Duvall kills one of the two and yet ends up abandoning his human identity and flying off with the other. This was from the Outer Limits if I'm not mistaken -- that was a great show also.