McAllister found the Red Barn (operated by Visualize), and he kills most of the members.  Two survived the Red Barn, but one was killed - in a struggle.  I suspect two people were "die-hard" Visualize members, and the other two didn't care.  The one that is left could be Haffner or Smith, but is most likely involved in law enforcement.  McAllister could be Lisbon's uncle (her mother's brother), and he set out to kill Brett Stiles.  Jane crossed him, when he publicly sought to capture him.  Red John wants to stay free, and he wants retribution.  Red John thinks his murders are for a good cause.  It is just like the season opener, when Dr. Wagner kills someone to provide money for African children suffering.  Wagner framed Red John.  Jane is allowed to live, since his wife & daughter were executed.  His survival is humilation, because Red John believes Jane needed to be punished.  Red John sees Jane's vanity as his weakness.  However, Jane was raised as a Carnie, so he can only be vain.  Red John merely drives Jane to be more vain, eventually.  Jane worked for Lisbon, and he closed cases.  Red John was planning on killing Jane, if he didn't close cases for Lisbon.  Lisbon is the key to his survival.  McAllister said he was sorry, but he wanted to tell Jane that Lisbon is the person helping him.  Those people (in the FBI) that help Red John, they are helping Lisbon be covered by any "blow back" from the Red John leaks.  She didn't intend to help Red John, but she used MCAllister as a crutch.  He is her family.  Red John took an apprentice with him, after Red Barn.  The apprentice is still out there.  In fact, the apprentice could be Lisbon.  McAllister could have used her to get closer to Stiles, but he got to the farm. Perhaps, she was raped by Visualize members (instead of the dead mother theory) - on the farm.  She fought back, and she killed the first Red John victims.  Red John is someone who will take responsibility for what happened.  She cant say what happened.  Local law enforcement knows about it, but they wont say.  Stiles wants them to stay quiet.  They keep all the evidence, in case stiles breaks his promise.  His promise to make up for his indiscretion.  He doesn't want any bad publicity, so he helps every cop that knows about the drugging.  Most of the evidence is circumstantial without the victims testimony and the police reports.  They say it was Red John, and nobody looks at Lisbon or whoever killed those people.  Either way Visualize & Red John crossed paths - in the Red Barn.  It was Red John's supposed first time killing.