Spoilers- Timeline of Red John's demise.
Partridge is irked by flies in the desert. Partridge remembers Bosco's lead would give his identity away now. Partridge goes and kills his identity in case Bosco told Jane. Jane's anger and guilt subside after the Cody Benbow case reminds Jane it was his fault his wife and daughter died. Jane remembers Bosco's lead, and remembers Partridge was irked in the desert.
Too late. Partridge has killed his identity. Jane realises Partridge remembered Bosco's lead too. Jane realises Bosco told him the lead with his dying breath. Jane decides if he pretends he never heard what Bosco said, he could pretend he doesn't know who Partridge is, and Partridge would believe that Jane didn't know he was Red John.
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Chubby woman in red pictured with her hands in front of her clapping, after Bret Stiles yells "I shall return." She's the woman feeding pigeons.
Brett Partridge uses people from his father's organisation. He sent the spy, made up to look like himself (uses the watch he wears in desert) , to see if Patrick knew that he was Red John. It was a dumb plan. Patrick saw her wrists and knew it wasn't Brett. But he pretended to think RJ left a file with Sophie Miller, so the spy would misinform RJ that Jane was still looking.
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RJ hires a PI to see if he could get any clues from the team if they know RJ is Partridge. They obviously don't know. Then for confirmation RJ kills the PI. The EMT is on the scene very fast... He watches Patrick's reaction. Patrick leans in and wipes the blood. The EMT tells Partridge of his reaction. Partridge thinks he's safe. The 3 dots is a trick, Partridge thinks he's conning Jane, because he knows more than 1 suspect has it.
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Patrick gathers all the suspects. Partridge writes to his father because he knows Patrick is gathering the suspects. Stiles doesn't have the tattoo. Stiles is safe to go ... or so Partridge thinks. Co-incidence that 2 cold cases on Stiles come up at the same time RJ sends the L. Martins video? No.
At the house, Jane knows the 3 with the tattoo are good guys- inside agents on Tiger Tiger (there's an absolutely, massively long explanation for this).
Patrick wheels around and shoots Ray Haffner. Then Patrick gets information from Stiles on where Partridge lives. Bertram, Smith and McAllister kidnap Stiles. A car (with those 4) coming opposite to Lisbon's stops and warns Jane she's coming. Jane sets up the explosion as Teresa arrives to get away with the murder of Ray Haffner and the kidnapping of Bret Stiles. He fakes McAllister's death as he is not under protection from Homeland as Smith and Bertram are.
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Stiles revealed RJ's house. It has a lemon tree just as Patrick said in an extra scene of the pilot. Same night, SWAT goes to RJ's house. A RJ mole is in the SWAT team. So they warn Partridge and Partridge runs away. Patrick enters RJ's house, sees pictures and flashback scenes occur of Partridge in the carnival.
So RJ gets away. No matter. Jane has Stiles + just forced RJ out of his home.
Next day Jane goes public. Jane tells CBI Red John bombed his house.
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Partridge has lost. His only chance is to appease Patrick. He exposes himself to Patrick in daylight in a beautiful park. They're alone together. Jane chases him and slays him in the sequence of several minutes. The killing scene is very intimate. Dead John.
