A man breathes heavily as he opens the gates to a park. A clown follows him. At one gate, there are chains around it, trapping him. The clown takes out a revolver, shoots the man, then takes a heavy-duty bolt cutter and clips off the man's right index finger.
Lisbon and Jane arrive on the scene, and find the man was Noah Kitt, age 32. A convenience store owner heard the shot and caught a glimpse of the killer. They meet the local police chief, Alice Hambrick. When asked why the CBI was called, he points to a long list of clowns that were picked up from the description. Apparently, there's a clown convention in town.
After interviewing some of them, Van Pelt finds that they're all people responding to an advertisement for a part for a clown, which specified that the people interested should come dressed as clowns. But, Patrick knows it's all just a smoke screen, so while Van Pelt keeps up questioning the dozens of clowns, he and Lisbon go talk to Noah's wife, Daphne Kitt, and his brother.
They watch a video of Noah talking about a complex math problem, trying to get his confidence up enough to become a teacher. Noah's brother says that Noah was a mathematical genius that graduated at 15, got a degree at 17, but had a problem addressing crowds. For a living, he published papers in mathematical journals, which didn't pay well, so they pretty much lived on Daphne's waitressing.
Noah tried day-trading, and spent most days at Aerials coffee shop day trading on his laptop, which is where he was the morning he was killed.
Jane notices that Noah had a chess game out, and Daphne recalls that Noah liked to play with a man named Tolman Bunting.
Jane and Lisbon go to the puzzle store that Tolman owns, (and find that he's that guy from Early Edition) and question him. He said that Noah was oblivious to peoples' feelings, which sometimes came off as rude, but was gentle. But with the last chess game, Noah said that he wanted to bet money on it, which Tolman refused to do. Before they go, Patrick Jane starts a verbal game of chess with Tolman Bunting, which his continues off and on throughout the episode.
Back at CBI HQ, Rigsby finds that Noah never owned a stock, and instead, he was e-mailing what looked like a random string of numbers to someone with the screen name Beastslayer949.
Daphne calls, and says someone's inside house. The CBI team enters, and finds that the house is trashed, like someone was looking for something. Jane notices that the kitchen, however, is undisturbed.
In Noah's bedroom, they find a safe which has a fingerprint scanner. Lisbon finds Noah's detached finger under the bed, and uses it to open the safe.
Inside the safe is a chess board, a Spider-Man comic book, and some papers. Daphne says that Noah lived in the house before she moved in, so she didn't know what was in the safe.
Jane notices that it's issue #42 of Spider Man, a collector's item which would be worth quite a bit, that the chess board inside the safe is made in China, while the one out on the table is an expensive set. Realizing that people don't tend to put cheap chessboards in their safes while leaving the expensive one out to use, he knows that Noah must be hiding something in it. Sure enough, inside the King piece is a locker safe with the number #42 taped to it.
Soon after, CBI discovers that Beastslayer949 is a man named Alex Moska, and Cho and Rigsby go to his apartment. After showing their badges and identifying themselves, Alex acts incredulous, and says that he wants to put on his pants before they come in (he's in a shirt and boxers). Knowing it's just a ruse to give him time to escape, Cho and Rigsby break open the door, and find him at the window. Still thinking the cop thing is a ruse, he shouts that whoever they are can have the $12,000 from the Boston Phillies Bet. When all he gets are confused stares, he finally starts to believe that they're cops. When he asks them again, and they again say they're with the CBI, he asked
"What's that?” "The California Bureau of Investigation" says Rigsby "What the hell's that?" he asks again Cho response "Like the FBI, but more conveniently located."
At HQ, they interview Alex, and find that the numbers Noah sent Alex were code for the picks of sports bets, which was Noah's real source of money instead of day trading. At first, the picks were spot on. But in the last few weeks Noah's picks went sour. Noah told Alex that he was having trouble concentrating for some reason, like he was pre-occupied with something.
Jane and Lisbon return to Tolman's shop, where he's talking to an Asian-looking girl with purple lipstick named Annika. When Jane puts his hand in his pocket to look like a gun from an old movie, she draws her gun and points it at Jane, causing Lisbon to draw her gun and point it at her. Tolman orders Annika to stand down, and Jane asks why a puzzle shop warrants an armed bodyguard.
He takes them to the back of the store behind a hidden doorway, and reveals that he's head of a group of coders for hire, basically mercenaries who will code encryption and decryption for anyone if they pay well. Within the last few months, Tolman offered 2 million dollars to anyone that was able to create a universal hack - some program that would be able to decrypt any encryption in the world. Noah took the challenge, said that he succeeded, but then had doubts about the morality of the device. When asked about who is part of their group, Tolman mentions Alex Cromel in Amsterdam, and Oliver McDaniel in Clark Mental Health Facility. They go there and talk to Oliver.
He's nutty, going on about space lords, intergalactic wars, and shiatsu massages, while eating Spaghetti-Ohs, but he does provide some information. He met Noah in Grad school, but even then, Noah's ethics prevented him from taking a job for defense contractor, since Noah didn't work on anything that could hurt people, so he shouldn't have taken the puzzle in the first place. Jane shows him the locker key, but he says he doesn't know what it goes to. But while they're leaving, an alarm sounds, when they run back to his cell, they find it empty.
They put out an APB on Oliver, and look into how he escaped. Apparently, he jury-rigged a passcard with a guard's passcode, tripped the alarm, and hid in the guard's quarters before escaping. Looking up the facility's logs, they find many times that he's used the code to leave within the month, and he could basically could come and go as he pleased, usually at night.
Jane asks Van Pelt to find a nearby spa by the sea, inspired by Oliver's rantings about massages and his recordings of sea sounds, and when she does, he goes over there.
At CBI headquarters, they learn that Oliver bought a ticket to Brazil with guard's cellphone, and Rigsby and Cho go to the airport, but before Lisbon can follow, she gets a call from Jane and the spa, and goes there instead.
There, Jane tells her why he thought Oliver went to this spa, and further, he found that Room 644 had ordered 6 cans of Spaghetti-Ohs, all but confirming he's there. So Lisbon recalls the team, and they tail him. He goes to Pacific Park, an amusement park. A man dressed as a maintenance worker knocks Oliver out and dumps him between vending machines. They find the man at the locker room, prying open locker 42, and give chase as Jane goes to look in the locker. But the locker #42 is empty, and further, the key doesn't fit in locker #42.
As the rest of the team chases, the man heads to the beach, starts to run into the water under the dock, but loses his footing and pratfalls into the water. He's Mr. Bunting.
Jane tries locker 6, and it opens just fine. Inside is a small plastic toolbox.
Both Oliver and Tolman are taken back to CBI HQ. Tolman is almost immediately released, because of his legal connections, despite the felonies he's obviously committed (assault, property damage, and resisting arrest at the very least).
Oliver is still whack, in addition to being whacked, and provides no more helpful information. But, Jane bribes him with Spaghetti-Ohs to work on the device found in Noah's locker.
Afterward, they take the universal hacker to Bunting's house, and Jane demands first to test if it works, and second that if it works, $2,000,000 should go to Noah's brother and wife. He says he's brought an encrypted CD of Lisbon's personnel file with him to test it out. On first try, it does nothing, but Daphne moves close and flips a small switch in the device, and urges Tolman to try it again.
He does, and this time it decrypts the file, but instead of Lisbon's personnel folder, it's just a looping text of "My wife killed me". They take Daphne into CBI HQ.
Jane says that he had Oliver fiddle with it and disable it, and make the encrypted disk, because he knew it would be irresistible for Daphne to re-engage the device if she thought the money was at stake. But Jane was expecting that, and doing so would show that she was lying, and in reality she was very interested in Noah's work, and knew a lot more than she let on. Further, Jane says his suspicion was piqued originally when after the house was searched, the kitchen was left alone, since the kitchen was left alone, Daphne's domain, since she knew Noah wouldn't hide anything there.
Now it's Daphne's turn to tell her story.
When she met Noah, she hoped it'd be like in the movies, where an eccentric genius finds love and understanding and they marry and live happily ever after. Instead, it's days and days of silence from him, with no sex, and with her busting everything she had for meager tips at a waitress job while Noah made almost no money himself. She knew about the universal hacker, and watched him make it, and when he refused the money, she was a lot more angry with him than she let on. So, she put out the clown ad and put on a clown costume, not only because she knew it would hurt Noah like he hurt her with his silence, his cold personality, and his refusal to take the money for the universal hacker, but it would also be a good disguise and the ad would allow her to get away scot free even if she was seen. So, she followed and trapped Noah, shot him, and clipped off his finger. When the CBI came, she used an intruder scare as an excuse to ransack the house herself, but after she found the safe, and found there wasn't anything of worth in it (well, there was the comic book, but she didn't know how much that was worth), she left the finger nearby so the CBI might be able to follow the case in her stead and see where he hid the universal hacker. When it was found, at Bunting's house she assumed that Noah just left it off, and so tried to sneakily turn it back on so she could collect the money, unaware that Patrick Jane was expecting that she'd do that.
Bunting returns to CBI HQ with papers asserting his legal ownership of the universal hacker. But when Jane takes it out, it's broken to pieces, either by him or Oliver, and though it might be possible to repair, reverse engineer, or remake, at the very least it's going to take a lot of time and effort to do so. Bunting takes the toolbox pieces, but before he goes, Jane checkmates Bunting in their ongoing chess game.
In the Western alphabet, the 18th letter is "R", the 5th is "E" and the 4th is "D". The title, "18-5-4", therefore spells out "RED".