"He Dead" is the second episode of season four. When a billionaire crashes his small plane in the woods, Shawn and Gus join the search to find the wreckage, but they arrive only in time to hear his last words - he was murdered.
In 1987, Shawn comes downstairs with an ice bag on his head and a thermometer in his mouth. He is claiming that he is sick. His dad takes the thermometer out of his mouth and reads it. He tells him that he is is a dead man walking, and informs Shawn that he is thinking about giving it another try with his mom, and maybe even having a girl. Shawn confesses that he was faking the whole thing and that he doesn't want to have a BBQ with a neighboring family, because they are vegetarian. Henry then pretends to be sick too after he hears they will have tofu burgers.
Chief Vick calls Shawn and Gus to the forest to aid in the search for billionaire Warren Clayton's downed plane. They arrive at the wreckage before the police and find Clayton inside, barely alive. As Gus tries to call for help, Shawn notices a "Wiswall" insignia inside the plane. He also sees that the altimeter reads 118 and spots metal clip with a picture of St. Dwynwen on it. As Clayton starts to fade, he says something about wanting to make amends and be a good father. He manages to cough out the word "Waterloo," then in his last breath asks them to find out who killed him.
Shawn feels obligated to carry out Clayton's last wishes. So, using the Waterloo reference with his widow Alice, who says that's the name of the 18th hole at the club where he wanted his ashes scattered, Shawn gets himself hired onto the case. Alice invites them to dinner, where Shawn meets the housekeeper Rosa, and Clayton's son Garvin. Shawn sees a daughter in some of the family photos, but Alice says Nyna is no longer with them. Shawn is able to "divine" that Alice was having an affair with her tennis coach and, seeing a matching St. Dwynwen charm, the patron saint of lovers, around Rosa's neck, he gathers Rosa and Clayton were also having an affair. Not only that, but Garvin was recently cut off from his father's money. Shawn realizes that everyone in the Clayton household had a motive and Alice promptly fires them and has them chased off the estate by dogs. They then head to Clayton's club to find more answers. There they learn that Clayton ran a successful hedge fund and they meet Chad Wiswall, a golfing buddy who lost his plane to Clayton in a bet. But Wiswall says he was in Europe when the plane crashed. All he knows is that Clayton said he was going to use the plane to travel with family and bought a private hangar at the airport for them all to use. Shawn knows this means everyone in the family had access to the hanger and the plane.
Shawn and Gus head to the hangar where they learn that Clayton made an unscheduled four-hour stop in Bakersfield the day he died. They track his movements to an environmental non-profit called The Great Green Hope, where the director, Mrs. Thomas, tells them their company had been at odds with Clayton since she and her husband founded it, and that Clayton had come looking for an endorsement on a business move. Mrs. Thomas refused, the argument became heated and Clayton left. Shawn and Gus tell the cops about their new suspect, who it turns out has a pilot's license and could have tampered with the plane's altimeter. Also, the Great Green Hope is the sole beneficiary in Clayton's most recent will. Alice is relieved that the suspect is no longer a member of her family, until Mrs. Thomas arrives for the will reading and she turns out to be Clayton's daughter, Nyna. Once more, Shawn and Gus have to outrace dogs out of the estate.
Nyna tells Shawn she lost contact with the family years ago when she denounced their way of life and started a new one with her husband Charles. Her dad had come to make amends but she told him she didn't want his dirty money. She doesn't know who killed her father, but she did overhear Clayton on the phone with a golf buddy talking about a problem with his investments. Shawn and Gus go back to the club and talk to Wiswall, who tells them Clayton's hedge fund was just a Ponzi scheme. All of the money is gone. Wiswall is not sure who else knows the truth about the money, but he did keep all Clayton's falsified documents as proof for the SEC. Later, Lassiter and Juliet meet Shawn and Gus at Wiswall's hotel room to get the documents, but when they get there, they find Wiswall murdered and the documents gone. And Shawn now realizes who took them.
At Clayton's funeral, Shawn announces that the culprit is Charles, Nyna's husband. Shawn tells the crowd that after Nyna turned down Clayton's money, Charles asked him to keep the organization in his will. But Clayton refused and was going to change the will back as soon as he got home. Charles, who along with his wife has extensive knowledge of aircraft, tampered with the plane. He thought he was in the clear when Clayton died before he could change his will, but then he learned about the Ponzi scheme. Knowing that Wiswall was about to blow the whistle and freeze Clayton's assets, Charles killed him, too. The police arrest Charles, fulfilling Clayton's dying wish to Shawn.