Lassiter and Juliet try to get March, the head of Internal Affairs, to tell them who Cooper was investigating to get a lead on what really happened to him that day. But March can't give up any details – except for the fact that Cooper mostly monitored how police logged evidence, nothing super secret.
Just then, Juliet gets a report on the wire that Shawn and Gus got in a brawl with the locals up in Box Canyon. She now knows their location is no longer a secret and that the murderer can find them once armed with the knowledge of their whereabouts. Juliet tells Shawn about Cooper and how he monitored evidence logging and Shawn gets an idea that makes him think Cooper was investigating Pierce, an officer at the SBPD that may have been tampering with evidence.
Shawn stumbles into Eli's house. No one is there, so he does some harmless snooping. He sees pictures of the community over the years. Then in Eli's desk, he sees an address in Santa Barbara written on a scratch piece of paper, then he comes across Gus in the kitchen making out with Nicole. Shawn pulls Gus aside, worried that Gus is leaning toward possibly joining this bizarre hippie farm cult.
Meanwhile, it turns out Shawn was right about his hunch on Pierce. Lassiter and Juliet arrest Pierce and they are certain they can get Pierce to confess to Cooper's murder.
Thinking that the SBPD has their guy, Shawn wants to get off the commune and back to Santa Barbara immediately. But he knows Gus won't leave without putting up a fight, so he pulls Gus aside and asks him to join him at the Peace Ash. Gus agrees, and they get in the Blueberry to drive there, but instead, Shawn hightails it out of the commune. But on the way out, they notice a car hidden under branches – the same car that tried to run over Nicole back in Santa Barbara. Now Shawn believes that the killer is at the commune still. They head back and try to find Nicole to make sure she is OK. They thankfully find her unharmed.
Just then, Lassiter and Juliet show up. Lassiter explains to the people that there is a killer on the loose, and Eli's reaction is to get everyone to go to the "Barn of Truth" to talk about what is going on with the entire community.
Geoff takes the floor and releases a truth. He tells Nicole that when she went to Santa Barbara, he knew she wasn't going there to shop for bobbins like she said, but that she was instead going there to see a man. Nicole steps up to defend herself by saying she and the man never had a chance to meet anyway. Geoff then admits that he read Nicole's emails – all from a particular email address – an email address that Lassiter immediately knows who it belongs to. Lassiter then steps up and reveals that the email address Nicole was writing to belonged to Dan Cooper, an IA agent. The man that she went to go visit was the same man that she saw killed.
Now all eyes are on Geoff. His coming to Nicole's defense at the fruit stand, added with his admission of spying on her, leads Shawn to believe that it was Geoff who killed Cooper out of jealousy because he thought Nicole, his ex-wife, was leaving the commune for good to be with another man.
Lassiter, Juliet, Shawn and Gus head to Jeff's house and find the body of Cooper in his shed. They arrest Geoff for the murder of Cooper.
In Cooper's wallet they find a picture of a woman that Shawn saw in the pictures in Eli's house from earlier. Dot, a community member, explains that the woman in the picture in Eli's wallet is Cynthia and that she left the commune years back. Dot also reveals that Cynthia's life was ruined after she left the commune. From this, Shawn puts it together that Cooper was emailing Nicole to try to get info on the Eli and the commune – to find reason for why Cynthia's life was destroyed after she left it. From this, Shawn knows it wasn't Geoff who was the killer. He believes it was Eli.
Shawn interrupts group exercise to place blame on Eli for the murder of Agent Cooper. Shawn reveals his reasoning by relaying the fact that upon arrival to the commune, everyone is forced to sign a document that gives Eli power of attorney over them and everything they used to own on the outside. Shawn then says it was Eli that murdered Cooper because Cooper was trying to get info on Eli, whom he believed was the reason Cynthia's life was destroyed. And after Cynthia left the commune, Cooper made it his life's work to investigate Eli and take the commune down.
Eli was planning on taking everyone's money and eventually fleeing. The commune is furious and as a result turns on Eli and takes him down. Eli is arrested.
Nicole tells Gus that she is headed to India and asks him to go with her. From this, Gus finally realizes that Nicole is a bit too cuckoo for him and declines her offer.