This is a sub-theory. I believe it is important enough to stand alone. I am sorry to do this. But here's the link to a full theory with comprehensive explanation of the entire RJ plot so far:
http://www.whoisredjohn.com/See-a-theory-Red-John/6373
Patrick Jane knows who Redjohn is
I will tell you how he knows, but by itself, this is pretty insubstantial. Partridge is irked by flies in the desert. Patrick reads this. Bruno Heller said RJ likes the cold for a reason, duh. Later, Patrick remembers what Bosco told him about Redjohn + puts 2 and 2 together. Partridge knows Rebecca failed to kill Bosco, so pre-empts Patrick knows his identity. Hence Redjohn disposes of the alias "Brett Partridge" + lures Lisbon. Faking death is easy. He knows people. How does he have so much money? Well his father is Bret Stiles. Sorry... going off track.
By the end of episode 1, Patrick already knows that Redjohn is Brett Partridge. I will start using very weak pieces of evidence, and grow to use better evidence.
0. Expression on Partridge's face in the desert at the end of the scene
1. Patrick does not even bother to look at Partridge's body
2. Patrick calls Lisbon 4 times near end of episode 1. Ignored every time. He is still happy in the car. He knows who RJ is and think's he's won.
3. As soon as he gets to Lisbon he takes Partridge's blood off her face. For evidence later.
4. Once Partridge is found out, he, Redjohn leads Patrick to Sophie Miller. "Carmen Lee" is a trigger. It's someone Patrick remembers from the mental institution. The recorder is a clue too late: RJ's fear: Acaraphobia; A fear of insects/bugs. (Partridge irked by flies)
5. Patrick intentionally misleads Lisbon saying its acrophobia. He lies saying he remembered Sophie Miller from "hospitals/doctors". He doesn't want her hurt. RJ already sent the message noone else should be involved by painting Lisbon's smiley.
6. Patrick sees Redjohn. The woman feeding pigeons. It's a taunt. Patrick won't do anything, RJ has men placed to kill Lisbon if he tried. He stares at the pigeons for ages. Then when Lisbon is going to leave he says Sophie Miller might have left some notes. This is obviously Patrick showing RJ that he is distracting Lisbon. We know that Patrick knows Sophie vocally transcribes notes. He already has the recorder itself!
Full theory. CBA writing anymore...
http://www.whoisredjohn.com/See-a-theory-Red-John/6373
