Good one last week! There was a biological weapon that was being tested in Europe somewhere (I can't remember where, but two of the main characters for the week were former members of the IRA, so I'll make the assumption it was near Ireland). Sidney and Vaughn went undercover to stop the production and bring the villians to justice. Vaughn posed as a priest (sexiest priest I've ever seen, next to Matthew MCConaughey in Contact) to gain the trust of the female. She was a doctor at this hospital - her brother was the bad guy and bullied her into helping him. While Vaughn was trying to build trust, he shared with her (the weekly villian) his guilt/grief over having to kill his wife while the other agents listened in on their wire-taps. So...Sidney got all wishy-washy and her feelings for Vaughn intensified.
Really...nothing happened to make it a "must-see" show as far as moving the storyline along. If you were ever an X-Files fan, you'll understand if I put this episode of Alias in the same category with X-Files episodes that had nothing to do with the conspiracy. Just fluff. If you weren't an X-Files fan, then suffice to say...it's OK that you missed it, just catch it on the reruns.