As it rains, Dipper and Mabel play a game in the attic to pass the time. Then, Stan calls them downstairs to make fun of Gideon's latest commercial. The gang proceed to recall their past experiences and their mutual dislike of him, and soon after they hear Gideon break in and attempt to unlock Stan's safe. They confront Gideon, who initially does not take Stan seriously, but ultimately flees when Stan hits him with a broom and chases him out with it. Stan, as he locks his precious deed in the safe, defiantly says that "the combo to the safe is in the one place Gideon can't get to," which is his mind. We then see Gideon outside the shack at the window, staring in with hatred and seething rage. He turns and pulls out Journal 2. He then mutters to himself that his "mind isn't as safe as you might think, Stanford." Then he says it's time to unleash the journal's greatest weapon: the dream demon that is Bill Cipher.
Later, as Wendy and the Pines are watching a western movie, Mabel suggests they switch the movie to Dream Boy High, which the others refuse to watch. Terrified by a bat in the kitchen, Soos rushes into the living room, and Stan sends a reluctant Dipper to take care of the problem; Dipper ends up injured after the encounter. Afterwards, Mabel and Soos tend to his injuries while Dipper complains about always having to do the hardest chores. Soos replies that Stan's personality is one of "life's great mysteries," and Soos decides to investigate another such mystery: whether or not it is possible to lick one's own elbow. Stan shortly after calls Dipper to fix the clogged sink, which angers his nephew even more.
Meanwhile, Gideon performs a ritual to summon the dream demon, Bill Cipher, who engages in various antics before making a deal with Gideon: he will invade Stan's mind, and Gideon is to help Bill with an unknown favor later on. Mabel and Soos, who witnessed the entire occurrence while hiding behind a bush, rush back to the Shack to tell Dipper, who was in the process of sweeping while his uncle slept, what they saw. Dipper consults Journal 3 and reads of the dangers of Bill, and watches the demon descend upon Stan's mind. After learning that they can prevent Bill's chaos by traveling into Stan's head themselves, they prepare and recite the necessary incantation.
Inside Stan's mindscape, the gang explore a bit and meet Bill, who is expecting them. Mabel tries to tackle him but instead goes into and right back out of the mysterious creature. Dipper is shot with a laser by Bill; however, it doesn't actually kill him, and instead only creates a gaping hole in his stomach. Bill expresses his deal with Gideon and his power over the mind. Mabel remained skeptical, saying that he couldn't figure out what she is thinking, but is overjoyed when he brings her boy fantasy to life. After warning them, he enters the Shack in Stan's head in search of his sought out memory. After a bit of goofing around, the gang ventures into the psychological Shack to search through Stan's memories, which include: his time in Colombian jail, being a door-to-door vacuum salesman, his disastrous date with Lazy Susan, and more. While Dipper sneaks a peek at Stan's memories of him to find Stan's apparently disappointing, true feelings about him, the others—including Bill disguised as Soos—look for and find the proper door.
Bill reveals his true form, teases Mabel and Soos, and runs off with the memory, and when Dipper arrives shortly after, he expresses rage about Stan hating him. Dipper then refuses to offer further help, and the others go to confront Bill without him. As Bill is about to give Gideon the code, Mabel shoots the memory of the code out of Bill's hand and into the bottomless pit. This sends Bill into a fit of extreme anger, in which he establishes an arena to face Mabel, Soos, and Mabel's dream boys with his weapon of choice: nightmares. Meanwhile, as Dipper searches for an exit, he comes across the memory of Stan expressing his actual feelings toward Dipper, and after watching the rest of the memory, learns that Stan is only hard on him to prepare him to face the world. However, he is sucked into the memory, and the Stan within the recollection informs Dipper of the ability to do whatever he wants within the mind.
Dipper then realizes that he must stop Bill and rushes off. As the demon is torturing Mabel and Soos with their nightmares (a British dog man for Soos, and making Mabel ugly) and prepares to finish them off once and for all, Dipper arrives with the news of being able to make dreams reality and demonstrates the ability to his comrades via laser vision. Mabel decides to give herself the ability to shoot kitten heads from her arms, Soos utilizes a question mark beam from his stomach, and so forth. Just as Soos, the twins, and Mabel's dream boys are about to send Bill out of Stan's head, he stops them, warns them of an approaching evil, and leaves. Stan wakes up and thereby forces Soos and the twins out of his head. They are relieved to have gotten rid of Bill, but their relief is cut short as Gideon reveals that he used dynamite to obtain the deed to the Shack, which gives him ownership according to Gravity Falls' odd laws, and forces the "trespassers" out as he has Bud destroy the building. The credits convey the message of "to be continued."
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- Stan was into boxing as a child and teenager.
- Stan hides his arrest warrants under the carpet in the Mystery Shack gift shop.
- Stan was "the biggest wimp" on his school playground when he was younger.
- Stan had freckles as a child.
- Stan had braces when he was a teenager.
- One of Mabel's worst nightmares is losing her cuteness.
- Soos has nightmares of a British dog man.
- The explosion muffin that Robbie spray painted on the water tower appears again.
- Mabel mentions her date with Gideon in "The Hand That Rocks the Mabel."
- The cloning copy machine from "Double Dipper" appears in Stan's office.
- When Gideon goes to the page for summoning Bill Cipher, the Negative Twelve Dollar Bill reappears again after being first shown in "Irrational Treasure."
- Among the images that flash on Bill's body after he says that he knows "lots of things" are Nathaniel Northwest's statue and Trembley's Cove from "Irrational Treasure," Stan entering the room behind the vending machine as seen in "Tourist Trapped," the broken arm of the Gideon-bot from "Gideon Rises," and the Gravity Falls Maximum Security Prison, seen in "TV Shorts 1" and several episodes in Season 2.
- Also shown is a closeup of the stamp from the opening sequence's title card.
- Xyler and Craz from Mabel's fantasy in "The Legend of the Gobblewonker" appear in this episode.
- Memories of Stan include clips from "The Legend of the Gobblewonker," "The Inconveniencing," "Double Dipper," "Irrational Treasure," "The Time Traveler's Pig," "Boss Mabel," and "Land Before Swine."
- Stan's time in a Colombian prison, as mentioned in "The Hand That Rocks the Mabel," is seen in his memories.
- Stan's date with Lazy Susan, an outcome of the events of "Dipper vs. Manliness," is shown.
- Stan's secret behind the vending machine is addressed for the first time since "Tourist Trapped."
- Mabel shoots the memory of Stan's safe combo into a memory from "Bottomless Pit!."
- The beginning of Stan's relationship with Carla McCorkle, previously mentioned in "Boyz Crazy," is shown.
- Mabel's dream of having a human sized hamster ball from "The Legend of the Gobblewonker" is revisited.
- Ford Pines is seen sitting in the stands during Stan's memory of his boxing lesson, his face hidden behind a book.
- The swing set in front of the Mystery Shack in Stan's mind later appears again in the ending credits of "Not What He Seems", and is shown to have been frequented by the Pines brothers in "A Tale of Two Stans".
- Viewership: This episode was watched by 2.7 million viewers on its premiere night.
- In an earlier version, Bill made his appearance to Dipper in a dream.
- In Gideon's commercial, the "Lil' Gideon Jingle," after the words Lil' Gideon's Tent o' Telepathy, MT is written instead of TM, the symbol for "trademark."
- Before going into the kitchen to fight the bat, Dipper picks up a saucepan and a spoon, both of which are nicknames of the constellation the Big Dipper.
- The spell Gideon uses to summon Bill is "Triangulum, entangulum. Veneforis dominus ventium. Veneforis venetisarium." Roughly translated from Latin, it means "Triangle — I invoke you. I come to the defensive barrier of the mind. I will see the barrier destroyed."
- Dipper chants the following to allow them to enter Stan's mind: . . . . . . . . . Taken together, the incantation is nonsensical. See individual sentence translation by hovering your mouse over the phrase.
- When Gideon falls to his knees and his eyes glow blue he shouts something unintelligible. When played backwards he is saying, "Backwards message! Backwards message! Backwards message! Backwards message! Backwards message!"
- While remembering Stan, Bill flashes an image that matches Stan's tattoo.
- On Bill's page in Journal 3 the words "ATBASH," "CAESAR," and "A1Z26" are crossed off. These are the names of the ciphers used throughout the show.
- Bill refers to Dipper, Mabel, and Soos as "Pine Tree," "Shooting Star," and "Question mark," which are symbols surrounding his image on his page in Journal 2.
- In Stan's mindscape, the moon looks like his magic 8-ball cane.
- The code that Stan inputs on the vending machine in one of his memories, is different from the code seen in "Tourist Trapped" and other episodes later in the series. It consists of only four buttons in a triangle shape, while the 'real' code consists of five buttons in a bucket-like shape.
- In the memory of Stan as a child and getting bullied in the playground, just before he is hit in the face with a soccer ball, a sports team name "Jersey Vultures" is seen behind him.
- In the memory of Stan at the movie theater, the theater is called Bijou, a reference to the Bijou film theater at The California Institute of the Arts.
- The first view of Stan's memories where it shows many memories at an angle, the scenes show his fez without the yellow symbol.
- Before airing on Disney Channel, the episode was leaked on July 6th, 2013.
- In Stan's memory of him boxing as a child, a boy is seen sitting in the bleachers reading a book. This is quite possibly Ford Pines, as he is similar in appearance to his child self seen in "A Tale of Two Stans," and his face and hands are covered.
- When the six-fingered hand symbol appears above Bill as he gives his message before exiting Stan's mind, the symbol is a mirrored version of that which appears on the Journals' covers.
- When Gideon summons Bill, the trees in the background look like they have eyes.
- Originally, the plot was that Bill would enter all the characters' minds, but it was cut short to only include Stan's. Ideas that were planned for Mabel were later used for Mabeland.
- Mabel's sweater, a sunset, is meant to represent the series' turn from a lighter series to a darker series.
- The images Bill flashes in his body when he says that he knows lots of things are, in order:
- A cartoon of John F. Kennedy.
- A photo of three UFOs flying.
- A zoomed-in image of the Mayan calendar.
- An image of Journal 3.
- A NASA lunar lander on the moon next to the American flag.
- A zoomed in image of one of the universal portal pages of the journals.
- A close up of a skull next to a lit candle.
- The Pyramids of Giza.
- Stan entering the secret code in the vending machine.
- The bigfoot-like creature from the main title theme.
- Part of the Zodiac.
- An enlarged image of a crop circle.
- Trembley's Cove from "Irrational Treasure."
- Nathaniel Northwest's statue.
- A zoomed in image of the stamp from the main title.
- Three gauges from the underground laboratory.
- The broken arm of Gideon-bot from "Gideon Rises."
- The Gravity Falls Maximum Security Prison.
- Then it repeats the UFOs and the Mayan calendar.
- Mabel calls Bill "isosceles monster". In the book Dipper and Mabel and the Curse of the Time Pirates' Treasure!: Select Your Own Choose-Venture, it is strongly implied by the Axolotl's poem about Bill that he's an equilateral triangle: the first verse says "sixty degrees that come in threes", and equilateral triangles have three internal angles of 60° each. This would mean that Mabel is correct, since all equilateral triangles are isosceles, according to the modern definition in which an isosceles triangle is one that has at least two equal sides.
- Stan's mindspace version of the Mystery Shack has "PBVWHUB VKDFN" over the main entrance, which is a caesar cipher for "MYSTERY SHACK."
- In front of Stan's mindscape version on the Mystery Shack is a Pitt Cola machine that has "SLWW" written on it, which is a Caesar cipher for "PITT."
- The top of the dreamscape Shack has a broken off sign that says "OAUVG." Once decoded it reads "MYSTE." However, instead of the usual three letters used in most of the show's caesar cipher, it is decoded using only two letters back.
- In one shot of the hallways in the mindscape Mystery Shack in the production art, "EWTUG AQW OCTKNAP" is carved into a wall. Decoding it using two letters back translates to "CURSE YOU MARILYN." However, in the actual episode, this message is edited out.
- During the end credits of this episode, there is a cryptogram that reads "20-15 2-5 3-15-14-20-9-14-21-5-4..." Once decoded, it reads "TO BE CONTINUED..."
- In yellow behind Bill Cipher's name is a message that reads, "." Once decoded, it reads, "LIAR MONSTER SNAPPY DRESSER."
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