A short sci-fi movie about earth pilots being held by aleins trying to get info. You think they are turning the female pilot into an alein but, they're turning the alein into a human to get info. About the earths plans.

It's an episode of The Outer Limits (not the old one). I think Robert Patrick starred in it?

ETA: Confirmed. An episode called The Quality of Mercy from 1995, and co-starring Trek's Nicole de Boer. Written by Brad Wright and directed by Brad Turner, both veterans of the Stargate franchise. Note that Patrick played the same character in a later OL episode.