Teresa Lisbon is dead.

Patrick Jane is currently in an asylum for the insane.

Lisbon died at the hands of Red John at the end of S6E1.  How else can we explain why RJ didn’t kill her?  RJ always draws the smiley face when he kills and it is present at Lisbon’s death site, on her face.  A very personal message for Patrick Jane.  Jane at that point loses his sanity and begins to hallucinate.  He wants to believe that it is drawn on her face because he can’t deal with the responsibility that he is cause of the death of another who is so close to him.  He wants to wash off the smiley face because he wants to wash away the reality of Lisbon’s death and believe that Lisbon is still alive.  Are we to believe that RJ is afraid of birds or that he just wanted to show Jane that he is in control of the situation?  Jane has been hallucinating everything from S6E2 on.  In S6E2 he believes that his original psychiatrist Sophie Miller is murdered by RJ but the murder is not typical of RJ.  A note is placed on the refrigerator and her head is placed in the oven.  RJ is always proud of his work and as Jane has stated, the smiley face is always the first thing you see because he is proud of his work.  Jane is back in the mental hospital, and he refuses to accept that Sophie Miller is again treating him.  So, he believes that RJ has killed her but in a way which alerts him subconsciously that the murder is not real.  As Jane has stated before, he has revealed things to Miller he doesn’t remember and during his first mental breakdown she was able to analyze him deeper than anyone has ever been able to.  A secretive man like Jane would not be comfortable with anybody understanding the true Jane that well.  E3:  Jane dreams that Rigby and Van Pelt get married, moving on with their lives in much the same way that his subconscious (through Charlotte) tried to tell him to move on.  E4:  Jane's subconscious reveals to himself that Hightower is involved with RJ (her statement that RJ is cleaning house).  E5:  Why would RJ need to bug CBI?  He has access to the building (if we believe it is McAllister) because he meets with Bertram and it was not presented as an unusual event for him to be in the CBI Building.  The private detective who approaches Cho looks like Summer and this is either RJ showing he has the ability to influence Cho or Jane believing that Cho is not the rock of the group.  E6-8:  they speak for themselves.  They wander like a hallucination.  How would Jane contact and set up the meet in his house as quickly as he did, in two days.  He is able to contact Stiles and “convince” him to attend the meeting.  Why would Stiles attend?  It is not to his advantage and places him in Jane’s control.  Why the time between the shot and the explosion?  The time sequence is off in these episodes and they suffer from being rushed and contrived to get to the house.  Then the episodes suddenly slow down and we are to believe that Jane is being held and prevented from getting to the final meeting place?  Then the ridiculous chase scene?  Why no fundamental answers to the RJ mystery?   

The new beginning or two year break.  Huh?  A new beginning with all of the old characters?  The new characters they’ve added:  Abbott who is suppose to be a FBI supervisor but is really the hospital administrator who we barely see.  Fischer who is suppose to be his FBI handler but is really the new psychiatrist who tries to first reach out to Jane (the island) and then when that is not affective, she exerts her power over him by trying to control him (the strict Fischer at the FBI office).  So who is with Jane at the FBI?  Cho and Lisbon.  This is to re-enforce the concept in Jane’s mind that he is not responsible for Lisbon’s death, but wants to believe she is still alive.  The idea of the FBI shutting down the CBI makes no sense.  How can a federal agency close a state agency?  Can’t be done.  But if Lisbon is dead, then the CBI team would have to disband.  Lisbon is the glue holding the team together.  When she was replaced by Hightower, Jane did everything in his power to have her re-instated.  If Jane were responsible (at least in his mind) for Lisbon’s death, it would close his relationship with the CBI.  He has far more information on RJ, at this point, than the CBI does, he is only still at the CBI because of Lisbon and the stray piece of information which comes their way.  He promised to keep her safe in the first season and has failed.

So Jane kills McAllister and then goes off to an island for two years where no one can find him.  Yet, Fischer is not only able to locate him, but is able to strike up a personal relationship with him.  It is as if Fischer has joined the hospital staff (after two years?) and is introduced to Jane and he relates this through his belief that he is on the island.  But that relationship is limited and then she reveals her true self, that of a person with power over Jane who tries to control him (the drugs to bring his psychotic events under control).  Again, she is a person who is in Jane’s life but not willingly in Jane’s life.  He sees her on a daily basis but Patrick Jane could not read her for who she is?  An admission from his subconscious about where he really is.   

How can we explain the lack of public reaction to Jane murdering a second man (who happens to be a police officer) and yet nobody discusses it (apart from Abbott and Fischer)?  This never made the papers?  Lisbon is OK with this even though she has always maintained that Jane would not kill RJ?  Not only did Jane commit a revenge killing, he did it twice.  That wouldn’t be national news?  Wouldn’t Karen Cross want to interview him, hold shows about Jane and his actions?  Make as much out of this action as possible to revive a career that Jane messed with? 

So Lisbon is dead and Jane is back in the mental hospital. 

Finally who is Red John?  I would suggest that RJ is Brett Partridge.  He’s not dead because he killed Lisbon.  He is the only other person we know was in the house even if it is implied that there is someone else.  That someone was created by Jane's mind.  Partridge has been battling Jane from the very beginning.  The RJ who is the master manipulator allows the rest of the world to know him as Brett Partridge.  Jane insulted him on TV and RJ killed his family.  Jane is condescending to him (as Partridge) every time they meet at work.  As Partridge, he resents the relationship Jane has with Lisbon.  He lures Lisbon to the abandon house and then kills her.  His motive is to prove to Jane that he is smarter and has won the game the two have been playing for ten years. 

The season finale will be Partridge coming to the hospital and saying in the RJ voice “Hello, Patrick.  I told you I’d be back to visit.”