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 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 to her annoyance, and Dipper learns that Robbie is still unable to get over his breakup with Wendy, 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 feelings for her, but ultimately fails, instead he invites 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 ask to what caused the damages, Stan, not wishing to reveal the zombie incident, lies and says it was a "big woodpecker." He then bribes the man, who accepts. He wonders 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 — a hiding spot under a tree. Wendy then arrives and talks about how she had 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 on Wendy, but he dishonestly informs her that he is over her, though she does not believe him.
Wendy points out a branch that resembles a lever. As Dipper tries to think of a way to reach it, Wendy easily climbs up to it using 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 turn 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 closing 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 so 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 quickly 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 asks for a sign, to which one Wendy simply winks whereas the other uses the zip-and-disposable-key gesture first seen in The Inconveniencing. Dipper, realising which Wendy is real, stabs the shapeshifter in the chest, who howls out in pain while leaking a greenish blood and returns to his true form. 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 reiterating 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 that channel again.
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- Robbie is still sending persistent text messages to Wendy.
- When Wendy was younger, her dad made her compete in lumberjack games, which she did very well at.
- Wendy attends Gravity Falls High School.
- Wendy has always suspected Dipper's crush on her.
- The author is male.
- The author engaged in experiments during his research.
- The author has six fingers, same as the cover of the journals.
- The author "hasn't been himself" for 30 years.
- The computer owner's first initial is "F."
- While watching Nearly Almost Dead But Not Quite!, a zombie movie, Dipper mentions that it's a lot less scary once you've fought zombies yourself, referencing the previous episode, "Scary-oke."
- Stan has hired a construction crew to fix the damages caused by the zombies after the events of the previous episode, "Scary-oke."
- Robbie is still not over Wendy (first revealed in "Gideon Rises"), following their breakup in "Boyz Crazy."
- Dipper, Mabel, Soos and Wendy return to the original hiding spot of Journal 3 as seen in "Tourist Trapped."
- Wendy meets up with them on the same bicycle and wearing the same helmet she had in "Gideon Rises."
- Wendy uses the zipped lips gesture first used in "The Inconveniencing," and later uses it to prove she is the real Wendy while fighting the Shape Shifter.
- The Shape Shifter takes the form of several creatures documented in Journal 3:
- Wendy mentions she can hear the things Dipper whispers under his breath, which he does so in "The Time Traveler's Pig," "The Deep End," and "Boyz Crazy."
- When telling Dipper how much their friendship means to her, Wendy claims she'd possibly throw herself down the bottomless pit if it ended, referencing the location featured in the episode by the same name.
- The final form the Shape Shifter transformed into was claimed to be Dipper's final form. In "Northwest Mansion Mystery," when Dipper is turned into wood, he took the same form. However, he was restored afterwards.
- Dipper's "final form" appearing in Northwest Mansion Mystery sparked a theory that, when Dipper was restored from his wooden form, he had secretly been taken over by Bill Cipher and was being impersonated by Bill. This was, of course, debunked when Weirdmageddon (event) occurred and Bill was revealed to be possessing Blendin Blandin.
- Viewership: The episode was viewed by 0.9 million viewers on its premiere night.
- "Into the Bunker" is the first Gravity Falls episode to originally premiere on Disney XD after the show was moved to that channel from Disney Channel.
- A small clip of this episode was shown at the 2014 LA Film Fest.
- The author planned to inhabit the bunker through the year 2070. This is despite the fact that Bill mentions he won't "get a heart attack till he's 90", meaning this would happen around 2050
- Mabel says that the bunker is "not as creepy as Dipper's internet history." According to Bill Cipher, Dipper's internet history contains "A LOT OF PICTURES OF REDHEADS!" 
- When the episode airs in syndication on Disney Channel, the scene in which the Shapeshifter transforms into a combined Dipper and Mabel is cut, as well as Soos' line of dialogue "Good luck sleeping tonight." The sequence in where slime drips from the Shapeshifter has also been shortened. Due to censorship guidelines, the scene in where Dipper accidentally lays on Wendy's bra is cut, along with Wendy's line "Don't feel itchy, man," as well as when Wendy kicks the Shapeshifter disguised as her in the breasts, and the scene wherein Dipper attacks the Shapeshifter disguised as Wendy in the lower chest area was also cut. The episode continues to air normally on Disney XD, however.
- Before the Shape Shifter is completely frozen, he transforms into Dipper and strikes a horrified pose. Dipper is turned to wood in the same pose in "Northwest Mansion Mystery".
- The Smez dispenser bears a great resemblance to the British dog man.
- During the ending credits of this episode, there is a cryptogram that reads "OOIY DMEV VN IBWRKAMW BRUWLL." Once decoded using vigenère cipher, it reads "WHAT KIND OF DISASTER INDEED."
- Found on a barrel in the bunker, the keyword is: "SHIFTER."
- Next to the author's Hiding Spot page, there is a binary code that says
010100000111010101110 1000010000001100001 011011000110110000100 000011100110110100101 11100000100000011100 000110100101100101011 000110110010101110011 00100000011101000110 11110110011101100101011 10100011010000110010 10111001000100001
- In the previous episode, Dipper's blacklight showed the edge of the very same Blind Eye symbol on that page.
- In the Cryogenic Tube section of Journal 3, there is a cipher that says "," which translates to "AM I ME? IS HE ME?."
- On the following pages, it says "" which decodes to "ICE ICE BABY."
- The page section revealed at the end of the episode says, "15-11-8-6-9-8-19-6 3-5-19 9-18 11-23-21-16-15-10-19-6-25 21-9-3-12-20" on the left and on the right says, "12-19-23-20 4-9 3-4-4-19-6 21-23-4-23-5-4-6-9-8-16-19" After being put through all of the ciphers, it translates to "IMPROPER USE OF MACHINERY COULD" and "LEAD TO UTTER CATASTROPHE."
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