Echo and her pals wake up in their pods prematurely. They get out and think they're either lab rats or in something out of a Saw movie. Eventually they are let out of their room and they see other Actives in their Inactive state. They decide to try to blend in to figure out what's happening.
Blending in doesn't quite work, but it's OK because it was the House experimenting on them. They want to see what would happen if the actives "woke up". Well, what happens is they remember a mix of real-life and engagement memories. Sierra remembers being raped by a client. Victor and Sierra are still attracted to each other. November (Mellie) remembers having a daughter and knows where she is... a cemetery.
At some point, those rogue Actives all fall asleep and are collected by Handlers and Agents. They were programmed to fall asleep when they got closure on their bad past events or desires. The doctor's theory was that this would help with the glitches they've been experiencing.
This was the first show that didn't have your typical mission-goes-wrong story. And I kind of missed the formula actually.