Dipper and Mabel Pines arrive in the remote town of Gravity Falls, Oregon to live with their Great Uncle Stan over the summer at his tourist trap, the Mystery Shack. Dipper begins to discover the town's paranormal side when he discovers a mysterious book detailing strange occurrences that have happened in Gravity Falls, and when he suspects that Mabel's new boyfriend might be a zombie.
It's fishing season in Gravity Falls and Stan is looking at Dipper and Mable to be his “fishing buddies,” but they'd rather go with Soos on an expedition to find a legendary sea monster known as the Gobblewonker. Meanwhile, Grunkle Stan tries desperately to find replacement “fishing buddies”.
Grunkle Stan learns his wax sculpture of Abraham Lincoln has melted, and Mabel makes a wax sculpture of Grunkle Stan to replace it. Next day, they discover someone has stolen the new sculpture's head. Dipper and Mabel set out to find out who did this crime.
Dipper and Mabel check out Grunkle Stan's arch enemy, evil psychic Lil' Gideon, during one of Tent of Telepathy shows. The little brat becomes obsessed with Mabel and decides that she will be his girlfriend, despite her repeated objections. After she gives him a final brush-off, Gideon invokes his psychic powers and declares revenge on the Pines family.
Dipper develops a crush on Wendy and attempts to portray himself as a mature teenager (he is really 12 years old, but is passing himself off as a 13-year-old) so he can hang out with her and her friends. But when Dipper, Mabel, Wendy and Wendy's friends visit an abandoned convenience store, they discover it is haunted by elderly ghosts who hate teenagers.
Dipper is haunted by his lack of manliness, so he goes on a quest to become a man with the help of a gang of Manotaurs he meets. Meanwhile, Mabel tries to teach Grunkle Stan how to be more of a ladies' man and capture the heart of the waitress at their local diner, Lazy Susan.
Dipper agrees to work the door at Grunkle Stan's big party, but he'd rather be inside flirting with Wendy. He uses a creepy copy machine to make duplicates of himself so he can do both, but the fakes all turn on him. At the party, Mabel competes against rich snob Pacifica to be crowned queen.
The kids try to expose Pacifica Northwest's fraudulent claim that her great-grandfather was the founder of Gravity Falls. Meanwhile, Mabel tries to prove that she can be serious, but learns her silliness can help. Once they figure out the truth, the kids are about to be sent to a government facility in Washington D.C.
Dipper uses time traveler Blendin Blandin's time machine to undo ruining his attempt to impress Wendy at a fair, but accidentally changes history for the worse, especially for Mabel. In the end credits, Blendon time travels to three scenes from earlier Gravity Falls episodes, wherein he is actually included.
Dipper is getting annoyed with Robbie when he accidentally breaks his cell phone and Robbie then challenges Dipper in a fight. Scared, Dipper finds a mystery that brings a character from an arcade game come to life, Rumble McSkirmish, but then realizes he must stop him before he kills Robbie. Meanwhile, Mabel tries to cure Grunkle Stan of his fear of heights.
Dipper discovers that he is an entire millimeter shorter in height than Mabel, so he tries to find a way to increase his height. Meanwhile, Gideon makes several attempts to gain ownership of the Mystery Shack, each ending in failure, until he sees Dipper and Mabel fighting over a crystal that can make objects shrink and grow, and uses it to shrink them.
Dipper and Mabel are trick or treating on Summerween, when a monster named ‘the Summerween trickster’ shows up. Dipper tries to impress Wendy by not treating.
Mabel bets Grunkle Stan she'll make more money at the Mystery Shack by treating people nicely than he does by being rude and cranky. He heads off to win a fortune on a TV game show while she deals with lazy employees and a real monster captured by Dipper. She soon realizes why Stan is such an unbearable grouch.
Stan shows Dipper, Mable and Soos the bottomless pit when a mysterious wind comes and they all fall in. While falling, they pass the time by telling each other stories.
It's the hottest day of the summer in Gravity Falls, and the new Gravity Falls Pool is now open. Mabel falls in love with a mysterious boy named Mermando who turns out to be a merman and needs her help so that he can see his family. Meanwhile, Dipper got the job of assistant lifeguard to impress Wendy and Stan fights with Lil' Gideon for the best seat at the pool.
Dipper wants his own room and when Soos finds one in the shack, Stan makes Dipper and Mabel compete for it. Meanwhile, Dipper has found out that the shag rug inside let's you switch bodies with whomever you shock.
When Sev'ral Timez comes to town, Mabel has her heart set on seeing them, but once she finds out that their actually clones, she decides to set them free, and realizes she wants to keep them for herself. Meanwhile, Dipper and Stan spy on Robbie, thinking he's brainwashing Wendy with his music.
A prehistoric beast snatches Waddles after Grunkle Stan throws him outside and it's up to Dipper, Mabel, Stan, Soos, and Old Man McGucket to go after the beast in order to save Waddles. Meanwhile, Dipper and Soos work out their friendship issues.
Gideon uses a mind demon to steal the deed to the Mystery Shack, and it's up to Dipper, Mabel, and Soos to stop home.
Dipper and Mabel try to defeat Lil' Gideon and win back their home.