Detective Lassiter is on a roll. He's closed nine cases in a row and since he's been on such a hot streak, the department hasn't had to call for outside help, leaving Shawn feeling superfluous and unwanted. When a dead body is found on the beach, Lassiter invites Shawn along to show him how it's done. At the crime scene, there is little to go on except puncture wounds on the body. Desperate to get on the case, Shawn looks at the marks and claims he knows who is responsible - a Tyrannosaurus Rex.
Even though Shawn threw out his theory as a guess, upon thinking about it further, he's sure the bite radius of the T-Rex actually matches the marks on the victim with surprising accuracy. The coroner says the man died from a hit on the head and then a fall onto a hard object. But Shawn, still convinced there's some truth to his theory, shows up at the morgue with a large papier-mâché dinosaur head to confirm the bite marks match up. The police think he's grasping at straws and tell him to seek help. Interim Chief Vick actually calls up Henry suggesting he set up an intervention for his son. But while Shawn is successfully convincing the psychiatrist of his psychic abilities, Vick and Lassiter show up to announce they have an ID on the victim. He's Christopher Franzen - a paleontologist.
Shawn and Gus go to the university where Franzen was a professor and learn that his paleontology department was in danger of being shut down. His assistant Ethan Robinson tells them Franzen was a terrible adviser, always tired and disheveled. When they show up at the victim's house, the cops are already there. They decide to check out the shed in the backyard instead, and after picking the high tech lock on it, they discover a collection of dinosaur bones better and more comprehensive than the department's, and serious digging equipment, some of which is missing. Shawn also finds something that looks like a large tic-tac-toe grid. Lassiter and Juliet figure one of the missing tools was probably the murder weapon, which most likely will be found in the bed of Franzen's missing truck. As they leave, Shawn notices many empty boxes from a fruit stand that is over 50 miles away, a long way to travel for a peach, no matter how good it is.
At the fruit stand, the owner tells them that Franzen was his best customer, coming by every night before closing on his way up the hill, coming back down very early in the morning. Shawn and Gus continue up the road in the direction Franzen went and discover a gate someone has been sneaking through. When they get to the other side, they find a large field in which many holes have been dug and filled in, but before they can investigate further, gunshots ring out, forcing them to run for their lives.
Shawn and Gus go to the police station to tell Vick about the farm when Lassiter and Juliet show up to announce they've found the truck and a bunch of damning evidence against Ethan. Shawn insists the answer still lies at Deacon Walker Farm. The cops tell him Franzen made several offers to Farmer Sullivan Walker to buy his land and was politely refused. The farmer was very forthcoming with the police and his story checked out. Unconvinced, Shawn and Gus go back to the farm with digging equipment. Franzen was looking for something. The holes were dug methodically in the exact pattern of the tic-tac-toe board Shawn found earlier. He realizes that the grid marked where Franzen had found what he was looking for, which turns out to be the only hole to be refilled by a bulldozer, the one piece of equipment a paleontologist would never use. They proceed to re-dig the hole where they discover a perfectly preserved skull of a T-Rex.
Franzen knew he'd find the dinosaur somewhere on the land, but Farmer Walker refused to sell it or let him dig there, for some reason turning down a potential windfall. When they go to ask him about it, Shawn also sees more refilled holes around the house, all of which were dug by a bulldozer. Which means, the farmer was digging as well. Just then Henry calls to warn him to stay away from the farm. He had a case out there years ago when Roger Deacon, the farmer's partner, went missing. He suspected Walker but the case went cold. Shawn tells him he's already at the farm and he's just solved the case. He calls the police out to the farm where he tells them that Walker killed his partner and buried him someone on the farm, but he forgot exactly where. That's why he couldn't let Franzen dig on his property and why, after he discovered him there one night, he had to kill him and dump the body elsewhere, recovering the dinosaur bones so no one else would come out with the same idea.
- The title is a reference to the Cretaceous–Paleogene (K–Pg) extinction event which wiped out the dinosaurs approximately sixty-five million years ago.
- While at the farm, Shawn references a movie with "all the holes" starring Sigourney Weaver and Jon Voight, and Gus can't name it. They're talking about the movie Holes, which Dule Hill (Gus) also starred in.
- The last name of the paleontologist in this episode is Franzen; there's a real life, world-renowned paleontologist named Jens Franzen.
- Shawn's statement, "This was not a boating accident," is a reference to the same famous line from the movie Jaws.
Juliet: Detective Lassiter is literally on fire.
Shawn: What kind of fire are we talking about? Michael Jackson in the Pepsi commercial fire, or misusing the word "literally" fire?
Juliet: No comeback? Shawn, that's slightly embarrassing.
Shawn [stumbling over his words]: Where'd you get that toot---suit, the...toilet store?
The gallery for 65 Million Years Off can be found here.