If I recall correctly that episode was called Kill Switch, and was written by William Gibson. I think it's from a season or two back.
From: Robert J. Bradbury <email@example.com> To: firstname.lastname@example.org <email@example.com> Date: Sunday, August 29, 1999 5:48 PM
Subject: Uploading meets X-files
>For those of you who missed it last night (or perhaps this
>morning), there was an X-files episode in which an AI
>pioneer, specifically mentions wanting to *upload*
>her mind and her boyfriend's mind so they could merge