The episode begins with Dipper over at Wendy's house watching a horror movie, Nearly Almost Dead But Not Quite! Dipper remarks that the film is a lot less scary after actually having fought zombies. He and Wendy proceed to mock the film as predictable and lacking common sense. Wendy receives a text from Robbie, and Dipper learns that Robbie is still unable to get over his and Wendy's break-up, despite his ex-girlfriend already having done so. Dipper then asks if Wendy is dating again, and Wendy jokingly states that she is seeing a stuffed walrus. He then attempts to admit his true feelings, but ultimately fails, instead inviting her to explore with him and Mabel. Wendy agrees to accompany them, and Dipper, upset, accidentally lies down on Wendy's bra (much to his horror).
Meanwhile, Stan supervises a construction crew repairing the Mystery Shack. When a worker inquires as to what caused the damage, Stan, not wishing to reveal the zombie incident, lies and says it was a "large woodpecker." He then bribes the man, who accepts. He ponders where the others are, and the scene cuts to Soos and the twins gathered around the spot where Dipper first found Journal 3. Dipper informs the others that he has uncovered a new lead on the author's whereabouts—his hiding spot under a tree. Wendy then arrives and talks about how she has been wanting to come with the gang for some time, but has been stuck cleaning up after her father. Mabel pulls her brother aside to tease him about his crush, but he dishonestly informs her that he is over it, though she does not believe him.
Wendy points out a branch that resembles a lever, and Dipper questions how to reach it. He suggests they make prototype "ladder shoes," but Wendy easily climbs up to it via her belt. She hits the switch with an ax and opens the entrance to a hidden bunker, and Dipper has the group promise not to tell anyone about what they may see. They descend the staircase and find an old fallout shelter, complete with rations to last at least to the year 2070. Dipper finds a recently opened can which prompts Soos' suspicion that the author may still be alive, and Wendy finds a hidden passageway behind a map of Gravity Falls.
The four arrive in a small room with various symbols in it, and Soos and Wendy comment on the "creepy" feel of it. Mabel jokes that Dipper's internet history tops the room's eeriness and accidentally pushes him onto a button, inadvertently setting off the security system. As the walls start pushing in, the gang turns to the journal for a solution, and they find they can open an escape hatch by pressing four symbols. They barely make it out, and Dipper's vest gets caught between the stones. As they inspect a surveillance room, Mabel goes to retrieve her brother's vest and finds a love letter he wrote to Wendy, and she encourages him to show his true feelings. Dipper declines her request, and she pushes him into a closet with Wendy.
Wendy tries to turn on the lights, but accidentally finds the path to a secret laboratory. The two question what the author did down there and spot various holes, which they soon learn were dug by an unseen creature. They try to inform Mabel of the danger, but she refuses to let them go until Dipper tells Wendy how he feels. Dipper dodges this and drags Wendy to find another exit. They hit a dead end, but are fortunately saved by a man claiming to be the author. Back in the surveillance room, Mabel and Soos play around with various equipment they find, including the author's lab coat and briefcase, when they uncover a note about a dangerous experiment (Experiment #210) called "the Shape Shifter." Mabel is horrified that she thought Dipper was lying, and she and Soos rush to save their friends.
Dipper's and Wendy's mysterious savior leads them deeper into the bunker, he informs them that he lost his research, and Dipper replies that he rediscovered it. Meanwhile, Mabel and Soos continue their advance, and Dipper and Wendy grow suspicious when they find the man is identical to the mascot on a can of beans. Their fears are confirmed when the man reveals he is a Shape Shifter, and that he wanted the journal to study creatures into which to transform. Wendy attacks the monster and causes him to drop the journal, which Dipper retrieves. The Shape Shifter follows the duo as they retreat, but is misled via a trick by Dipper.
Dipper and Wendy run into Mabel and Soos, though they are suspicious that they may be their pursuer in disguise. However, after observing their goofy behavior, they are reassured their friends are who they appear to be. Dipper worries that if the creature escapes, he could assume the form of anyone, and Wendy prepares to launch an attack on him. While the Shape Shifter looks for Dipper, his target and Mabel enter the room. The monster then transforms into a horrifying amalgamation of the twins, who lead him toward Soos and Wendy, who have prepared a water pipe to blast him. The pipe briefly stalls, and Wendy goes after the monster with her ax before getting hit with a huge burst of water.
When the flooding subsides, Dipper encounters Wendy's unconscious body and begins to cry over her, just as a second Wendy appears behind him. The form on the ground turns out to be the Shape Shifter, who engages in combat with the real Wendy. Dipper picks up Wendy's ax and comes to help her, but he is unable to distinguish between the true and the copy. He asked for a sign, and responds to the real Wendy's throw-away-the-key gesture by hitting her foe in the chest. Dipper and Wendy then force the monster into the cryogenic chamber in which he had previously been held, and he uses his last words to tell Dipper he will never find the author and Dipper's fate will be worst than he can imagine, before morphing into a screaming Dipper as his final form.
The group leaves and seals the bunker, and they reflect on the adventure. Soos comments that his face is tired from screaming all day, and Mabel hails the four as heroes. Soos opts to take her back to the Shack for a "hero's breakfast," and praises her idea to put syrup on their cereal. Dipper and Wendy stay behind to discuss Dipper's crush on her, and while the former prepares for the worst, the latter informs him that she always suspected it. While she's flattered she lets him down easy and assures him, by re-iterating how much his friendship means to her, that the situation between them is and will be fine. Mabel then comes back to reveal that she heard the entire conversation and apologizes for her pushiness. Soos meets them and states that he is disappointed that they did not find the author, but upon learning that the briefcase he recovered is actually the mysterious figure's laptop, he says he could fix it in a few days' time. Back at the Shack, Dipper and Wendy watch a terrible movie marathon, and Dipper comments that he never wants to watch the channel again.