As a car speeds down the road at night, Sheriff Blubs and Deputy Durland sit in their car and unsuccessfully attempt to do a maze. Durland is initially distraught by his failure, and Blubs tries to cheer him up by telling his partner that their time together is more than satisfactory as it is. Suddenly, a rumbling is heard, and an unseen flying creature rips the roof of the police car. Instead of reporting the incident, the two decide to take a drive in their makeshift convertible. The creature flies across the night sky, and the theme song plays.
In the following morning, at the Mystery Shack, Stan is taking a group of tourists through the woods to see various oddities, and Mabel takes advantage of the empty house by having a dance party with Waddles until her great uncle's return. When Stan finds the girl lying with her pet on the floor, he makes a sarcastic remark about her being weird, and the two mock Dipper's behavior in comparison with Mabel's. Next, Waddles proceeds to chew on Stan's pant leg, thus ripping it. This makes Stan annoyed, so he tries to send him outside, but Mabel scolds the old man for this proposal and walks away with her pig.
Meanwhile, Dipper and Soos are preparing to investigate the mysterious creature that had ripped off the police officers' roof, thought to be hiding in the woods. They prepare a trap involving the beast taking a piece of meat and subsequently activating cameras so that Dipper and Soos could obtain a picture of it. Back at the Shack, Mabel sees a commercial for a baby carrier that is also advertised to carry pigs, and she decides to get one for Waddles, and mistakenly trusts her reluctant, irresponsible, great uncle Stan to watch her pet.
Dipper and Soos soon return from their monster hunt, and Dipper volunteers to develop the film from their photos while Soos makes nachos in honor of their prevalence. While Dipper anxiously works to find a good picture of the beast and comes close to successfully revealing its existence, Soos instantly ruins the one good shot when he barges into the room to joke about eating all the nachos. The open door exposes the film to bright light, destroying the image. Dipper is upset and suggests that Soos, who claims to have been extremely excited by the nachos, should be more careful as he doubts that they will have another opportunity to photograph the creature.
Simultaneously, Stan guides a group of tourists through the Shack and makes no effort whatsoever to keep an eye on Waddles. However, he and his customers soon cross paths with the animal as they learn that Waddles has eaten Stan's fake unicorn made of corn (aka "cornicorn"). Disgusted by Stan's lies, the tourists storm off, and Stan angrily puts the pig outside to avoid any other potential losses of profit. Despite his initial derision of his niece's warnings, Stan is shocked when the same beast Dipper and Soos are hunting, a dinosaur, captures and flies away with Waddles.
Dipper and Soos, who have caught a glimpse of the flying beast through the upstairs window, rush outside to learn of the strange occurrence, and Mabel returns from her errand to be informed of her pig's fate after an initial silence. Stan twists his actual actions of leaving Waddles outside into a fantasy situation of the pterodactyl breaking into the living room, thereby interrupting Stan nursing the pig, and snatching him out of Stan's arms. Stan proceeds to describe him fighting off the creature, albeit without success. Mabel is heartbroken, but Dipper protectively intervenes and offers to help retrieve Waddles, and Soos joyously complies. Stan expresses doubt at first and suggests they relax, but the others convince him to come along.
The gang prepares Soos' pick-up truck for the big mission, and Dipper confides his disbelief in Soos' abilities on such a risky adventure after the man-child nearly runs his head over. Mabel agrees and tells her brother to let him down easily, but, Soos' enthusiasm renders Dipper unable to hurt his friend's feelings. Thus, the four follow the trail of yarn left behind to an abandoned church in the middle of the woods, where they meet Old Man McGucket, who tells them that he watched the creature enter the abandoned mines. They opt to go in, albeit with more opposition from Stan, and Old Man McGucket comes with to tell "weird, personal stories."
Within the depths of the mine, the group discovers various Jurassic plants and find various dinosaurs trapped in melting sap, which they deduce to be the beasts' method of survival. Most of them see the area as a danger zone, but Stan sees it as a unique business opportunity and envisions a theme park. However, he accidentally divulges the fact that he left Waddles outside unattended; this pushes Mabel over the edge, and she decides to never speak to her insensitive grunkle again. Soos tries to prevent them from arguing by remaining optimistic though his efforts prove ineffective when he ravels the yarn back up-- thus ending the clear-cut path-- and accidentally breaks their lantern. Dipper grows to a level of anger equal to his sister, and he and Soos start to fight as Mabel's and Stan's conflict escalates.
Old Man McGucket interrupts to say that he fixed the lantern, but he finds the pterodactyl standing behind him. He instructs the others not to make any sudden movements or loud noises, though he himself does both and causes the dinosaur to chase after them. They then try in vain to formulate a plan of escape, though their arguing hinders them from accomplishing this. Mabel hears Waddles from a nearby nest and races down a set of rickety old train tracks to get him, and the boys closely follow her. She has only a brief moment to celebrate the reunion before the pterodactyl returns and frightens Waddles, who runs into Stan and makes both of them fall into the pits below and into a mud puddle.
As Dipper, Mabel, Soos, and McGucket see the pterodactyl's egg hatch, they panic when it eats the old man. Down below, Stan tries to use Waddles as bait to distract the beast while he escapes, but he soon realizes how much the pig means to Mabel, and how much Mabel means to him, and warms up to the animal. He takes his actions a step further and acts as a human shield for Waddles and fights off the creature in a manner similar to his previous, untrue tale. Dipper and Soos make up when Soos admits to and apologizes for his mistakes, and Dipper and Mabel take his advice to follow him in a straight line, as the dinosaur's eyes are "so far apart" that it cannot see directly in front of itself, and the plan succeeds.
Soon, the trio sees Stan heroically fighting the adult dinosaur, and he even goes to punch the menace in the face as he had previously said he did. Stan's blows are powerful enough to literally send the dinosaur falling to the ground, and the others congratulate him, with Mabel and Stan bonding over Mabel's pet pig. But, the moment ends as quickly as it started, for the dinosaur manages to climb back up and chase after the Pines and Soos. They run through the tunnels back to their starting point and, since their rope is broken, try to use a geyser to shoot themselves to the surface. To speed up the escape, Soos punches the geyser to activate it, and the group finds itself wet and in various random places.
The rear of the church collapses into the hole, and the Pines exit the building. Mabel and Stan talk about the happenings, and play around with tree sap and ultimately get stuck. On the way home, Mabel, Stan, and Waddles sleep in the back seat, and Dipper and Soos are ecstatic to find an authentic dinosaur tooth in Dipper's destroyed vest. Dipper agrees to Soos' proposed nickname, the "Pterodactyl Bros," and Soos rejoices when he correctly pronounces "pterodactyl." The two disregard any danger of the other dinosaurs reawakening, and McGucket is shown to have escaped the dinosaur and the mine by eating his way out with his musical spoons. In the credits, Dipper and Soos watch an infomercial for "arm pants," which Soos was naive enough to order, and Mabel, Stan, and Waddles play a game of poker in which none of them follow the rules.
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- According to Mabel, Dipper kisses a pillow that has Wendy's face drawn on it.
- Dipper knows how to develop film using the analog process.
- Sheriff Blub's and Durland's patrol spot beside Gideon Gleeful's billboard makes a reappearance from "The Deep End."
- The photo Dipper takes of the pterodactyl is the same as a photo from the opening.
- Dipper's BABBA CD from "Dipper vs. Manliness" appears amongst the garbage.
- Mabel's bike and helmet makes its first reappearance since "The Hand That Rocks the Mabel."
- During the flashback sequences of when Soos messed up, Dipper is reading the Floating Eyeballs and Giant Vampire Bats pages in the Journal 3.
- The underground caverns with the dinosaurs were glimpsed in "The Time Traveler's Pig" when Blendin Blandin's suit malfunctioned.
- The ability for creatures to be put in suspended animation in sweets was established with Quentin Trembley (peanut brittle in his case) in "Irrational Treasure."
- Viewership: This episode was watched by 3.5 million viewers on its premiere night.
- The concept of "the real monster is you" by using a mirror as part of the Mystery Shack's exhibit, was also the subject of Alex Hirsch's art piece for Disney's "Some Kind of Monster" art show.
- When Soos opens the door, only the print is ruined. Dipper could have printed another from the negative.
- Stan lands in a coffin after escaping the abandoned mines.
- The articles Dipper collected on the mysterious creature covered stories about the patrol car's roof getting ripped off, sheep snatching, and miners going missing after uncovering the network of caverns.
- This is the 4th time Wendy doesn't appear, although she is mentioned.
- According to the Season 1 SoundCloud Soundtrack, this episode was originally/tentatively titled "Dino Cave Mystery."
- While Stan is fighting the Pterodactyl, he shouts "From heck's heart, I stab at thee!" This is a slightly censored quote from the Herman Melville novel Moby Dick. In the novel, Captain Ahab shouts this as he stabs Moby Dick with a harpoon.
- During Stan's fantasy sequence we see his back turned and his bare back. Where his burn mark should be is instead "OLHV," which has a remarkably similar shape to his actual burn mark. Once decoded using the Caesar cipher it says, "LIES."
- The cryptogram in the end credits reads "9-20 23-15-18-11-19 6-15-18 16-9-9-9-9-9-9-9-9-9-9-9-9-9-9-9-9-9-7-19!" Once decoded, it reads, "IT WORKS FOR PIIIIIIIIIIIIIIIIIGS!"
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