Stan continues to work on the portal while the Mystery Shack throws a grand re-opening party after the Li'l Gideon incident. Meanwhile, when Dipper meets two government agents, he tries to tell them about the mysteries of Gravity Falls by showing them his journal. When the agents don't believe anything written in the journal, Dipper ends up conjuring up zombies to prove to them he's not crazy. ("Scary-oke")
Dipper's journal pages lead the gang to the author's hidden bunker where they find themselves face-to-face with an evil shapeshifter whom the author raised from a mysterious egg. Meanwhile, Dipper finally builds up the courage to tell Wendy how he feels about her. ("Into the Bunker")
After being belittled by Pacifica one too many times, Mabel challenges her to a miniature golf-off which gets out of control when she and Dipper discover that living golf balls control the courses. ("The Golf War")
Mabel attempts to make the perfect sock puppet show to impress her new crush. Meanwhile, Dipper tries to figure out the password to the laptop found in the bunker, while Bill Cipher wants to make a "deal" with him. The deal involves Dipper and Bill switching bodies, resulting in Dipper having a non-corporeal form. He talks to Mabel through puppets and tells the truth to her. She and Dipper sabotage Bill and tickle him, eventually causing Dipper's systems to shut themselves off and defeating Dipper. ("Sock Opera")
After Soos promises his grandmother to find a date for his cousin Reggie's engagement party, Dipper and Mabel offer to help him. Eventually, he uses a dating simulator to help him talk to girls. However, Giffany, the girl in the game, obsessively falls in love with Soos and eventually reveals herself as a sentient, malicious and extremely jealous AI after Soos asks Melody, a girl who works at a meat stand, for a date. At the restaurant, which is an arcade, Giffany takes control of the kiddie robots, causing them to gain sentience. Soos fights Giffany by destroying her desk, ending the sentience. Meanwhile, Stan plans to steal a kiddie robot for the Mystery Shack. Stan steals a robot and heads to Las Vegas, gambling with it, where they are thrown out of a casino. ("Soos and the Real Girl")
In this non-canon episode, Stan tries to sell Mystery Shack merchandise to an unknown buyer by telling stories about each item he sells. Stories include:
"Hands Off": After stealing her gold watch, Stan is cursed by a witch and loses his hands.
"Abaconings": Waddles becomes smart because of a mysterious mushroom and soon becomes so smart he forgets about Mabel.
"Clay Day": Mabel confronts her fear of stop motion animation by fighting clay monsters. ("Little Gift Shop of Horrors")
Dipper, Mabel, Soos, Wendy and Old Man McGucket discover a secret society in Gravity Falls that erases people's memories of the supernatural. McGucket discovers that he founded the society to erase his own memories, but after erasing his memories too many times, he drives himself insane and amnesiac. Upset, Dipper and Mabel comfort him as Dipper gives him the computer from McGucket Labs that he found in the bunker and McGucket agrees to look it over. ("Society of the Blind Eye")
Blendin Blandin returns to face off against Dipper and Mabel in a futuristic, potentially deadly battle. Meanwhile, Soos is upset about his birthday, and Dipper and Mabel try to figure out why. While in the future, Dipper and Mabel steal time tape that sends them to Gravity Falls ten years ago to 2002. They discover that Soos hates his birthday because his father never showed up for his twelfth birthday, and vow to win the battle so that Soos can meet his dad again. They win the battle and are given a time wish and fate for Blendin. They decide to give him hair and his job back, redeeming Blendin, and allowing Soos to use the wish. Soos uses the wish to eat a slice of infinite pizza. Soos throws away his gift card from his twelfth birthday and assures the twins that the Pines are his real family. ("Blendin's Game")
Mabel takes matchmaking too far when she steals a love potion from a real Love God to use on Robbie and Tambry. Meanwhile, Stan decides to create a hot air balloon for the Woodstick music festival. Stan creates a hot air balloon, but things go awry when it burns on fire. Meanwhile, Robbie and Tambry's relationship redeems his friendship with Wendy and Dipper, who forgive him for his past actions. ("The Love God")
The Northwests hire Dipper to deal with a ghost that threatens to disrupt their party but Dipper soon finds out the Northwests' secret from that ghost. Dipper is threatened by the Northwest as Pacifica lets the townsfolk in to defy her parents and she realizes she does not want to be her swindling family, who swindle and steal from the poor, redeeming herself in Dipper's eyes. During the party, Candy, Grenda and Mabel fight over a boy they all want to date. ("Northwest Mansion Mystery")
After government agents take Stan into custody, Dipper and Mabel begin to question how much they really know about their Grunkle and must work out whether or not they truly trust him anymore. Finally, the portal is activated and the author of the journals is revealed to be Stan's long-lost brother, Ford, who emerges from the portal as Dipper, Mabel, Soos and Grunkle Stan look on. ("Not What He Seems")
Stan has to reveal his past to Dipper and Mabel, along with the secrets of his twin brother, Stanford "Ford" Pines. Stan's real name is actually Stanley Pines: thirty years ago Ford constructed the portal but was trapped inside it due to a mishap with Stanley, his estranged con-artist brother. Stanley assumed his brother's identity as "Stanford Pines", and spent the next thirty years trying to fix the portal to get Ford back. He was finally able to reactivate the portal after the kids discovered Ford's missing journals. In the end, the agents leave after having their memories erased, and Stanford decides to live in the underground lab under the Mystery Shack. Grunkle Stan makes him promise he will leave the kids alone after being told that he would have to leave the Mystery Shack at the end of the summer. ("A Tale of Two Stans")
Dipper finds his favorite board game called "Dungeons, Dungeons, and More Dungeons", and Great Uncle Ford joins him. When Grunkle Stan accidentally rolls Ford's Infinity-Sided Dice, the characters from the game come to life and capture Dipper and Ford. Meanwhile, Mabel, Grunkle Stan and Grenda try to watch the Ducktective season finale. ("Dungeons, Dungeons More Dungeons")
When Stan decides to run for mayor, Dipper and Mabel must make him a better candidate to increase his chances. They force him to wear a tie created by Ford that makes a better candidate, but when he finds out the truth, he abandons them. Meanwhile, Bud Gleeful, father of Li'l Gideon, runs for mayor as well, in an plan to get Gideon out of prison, and he blows up a mountain with Dipper and Mabel left inside. Stan rescues them, restoring his image with the public. However, he is prohibited from being mayor, due to his felony record. Due to Bud's exposed crimes, the job is given to Tyler Cutebiker. ("The Stanchurian Candidate")
Mabel and her friends go on a magical quest to get unicorn hair in order to protect the Mystery Shack from Bill Cipher. Meanwhile, Dipper finds out that Bill and Ford used to be partners and designed the portal together. However, Bill tricked him the whole time, so Ford had to shut down the portal. Bill has been waiting for the reactivation ever since, and once he gets his hands on the interdimensional rift created by the portal will mean the end of the world. ("The Last Mabelcorn")
Stan brings the kids on a road trip to ruin every other tourist trap in Oregon. Meanwhile, Stan tries to help Dipper get over Wendy. ("Roadside Attraction")
Mabel decides to plan her and Dipper's 13th birthday party, it's a big deal to Mabel because it also the same day they have to leave Gravity Falls, Ford however needs Dipper's help in sealing up the rift, Mabel who doesn't know about the rift lets Dipper go with Ford giving him matching backpacks and walkie talkies when they need help. Meanwhile, Ford reveals to Dipper the most surprising secret yet—a giant UFO which, according to Ford, crashed millions of years ago and is buried under the town. It was by using parts of this alien technology that Ford was able to construct the dimensional portal. Bill Cipher tricks Mabel into handing him the interdimensional rift, which Bill then uses to enter the physical world and open a portal from his own dimension. ("Dipper and Mabel vs. the Future")
The battle for the fate of the world begins as Bill Cipher and his minions are released from their dimension. Meanwhile, Dipper and Wendy try to save Mabel from a prison bubble designed by Bill and guarded by Gideon. ("Weirdmageddon – Part 1")
Dipper, Soos and Wendy enter Mabel's bubble to save her and discover an odd world inside of it. Meanwhile, Bill and his friends try to initiate the second phase of their master plan. ("Weirdmageddon 2: Escape from Reality")
Dipper and Mabel rally the town to fight against Bill Cipher and his minions in one final stand to save Gravity Falls from destruction. To save Dipper and Mabel, Stan and Ford switch places and Ford wipes Stan's memory to kill Bill. However, the kids and Ford remind Stan of his past through Mabel's scrapbook. In the aftermath, the Northwests become poor due to Preston Northwest pouring all of his savings into Bill's rule, McGucket buys Northwest Mansion, and Soos takes over the Mystery Shack when Stan and Ford leave Gravity Falls to search for anomalies. Dipper and Mabel leave Gravity Falls while Dipper narrates his adventures. ("Weirdmageddon 3: Take Back the Falls")