What episode was it when ...?

I think it was season 2 episode 4 "Belonging"

Sierra gets raped দ্বারা her handler (while in her doll state) in season 1 episode 6, 'Man on the Street'. However, like Yukari12 said, she also gets raped দ্বারা Nolan in 'Belonging', although when that happens she is imprinted.