I really loved this episode. I can see some of the points others made regarding plot holes or things that don't quite line up... but all in all it was a well written piece that sets things up nicely for the final episode in this arc, and I found the acting to be exceptional. I also feel like dribbles and drabbles of things that have been mentioned for years are starting to make even more sense.
Prentiss is in an impossible situation. She is bound by her previous circumstances and "oath" (referred to in 6:16 "Coda", during conversation with Tsia and Clyde in the courtyard while she is on her "late lunch") to keep what she knows from her current team. I felt it was very evident that she is not happy with this for many reasons. She does not quite trust her old team, especially Clyde. She feels the BAU could help with this situation, and her discomfort at holding back was very obvious to me in a number of situations. She is frightened for herself and them, and wants to confide in them to warn them and get their help.
However, Prentiss obviously fears for the safety of her BAU family. Even though they have no idea of her relationship with Doyle, they are in danger just by being associated with her. Doyle has made that clear. She doesn't have any idea of how info is getting leaked to Doyle, so she cannot trust that telling the BAU will not put them directly in his sights. She also seems to have a sense that killing Doyle may not be quite enough to stop what he has set into motion. Add to this the fact that she is exhausted and under great strain, well... her decisions may be brave and "kick-ass", but are not necessarily the best. Watching Prentiss's conversations with the rest of the BAU team was very moving. I felt I could see how torn she was each time. Garcia knew Prentiss had just told her something incredibly important... her reaction was exquisite, showing that she knows her friend is hurting deeply. (Did she sense that was a good bye, or fear for her friend's emotional state? I am not sure. Perhaps it was a huge realization that even Emily Prentiss has moments when she cannot compartmentalize.) Reid and Morgan obviously know something is bothering her. They both ask her, and in my opinion try to respect her while letting her know they are willing to listen. Reid opening up to her and Morgan reassuring her were both very touching. (I've always been annoyed by the "no inter-team profiling" rule, which has basically given everyone an excuse to not ask and not tell about stressors. Morgan, Garcia and Reid are all acting as good friends and colleagues, IMHO, when asking Prentiss what is troubling her. "It's psych 101", darn it!)
In the end, Prentiss is near tears as she looks around the BAU bullpen at her friends and colleagues, and quietly leaves. I was near tears myself, because I can only imagine what she thinks she is walking into, alone. Prentiss is, in her own way, as much of a "maverick" as Morgan can seem, and her need to do this on her own seems both noble and strong, yet reckless and foolhardy at the same time. One issue I noted people bringing up a lot (here and on other sites) is that the build up has been "too long". Well, this is a complex situation, and would not be easily told in one episode unless you get some backstory. And many little bits of the past seem to feed forward into this. Perhaps now we understand why Prentiss has learned to "compartmentalize better than most people." Hotch has told Morgan before that he needs to trust his team more... now Morgan knows what it feels like to have a team member hold back from him. Reid takes a chance and lets Prentiss in on his headache issues, and reveals he doesn't want to be "treated like a baby" by the others if they worry about him. Maybe he is learning to take care of himself properly; he can accept concern, but doesn't want to be seen as weak. (That is a hard thing for someone to figure out!) He's always struggled with that, so in my mind this is a step forward for him.
Two weeks until "Lauren"..... ugh, how to manage waiting so long!