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--->'''[[FamousLastWords Yuki:]]''' I'm lucky, so lucky for this. For you all. [[CallBack Imagine what... what would have happened if you two had never stayed in Gravity Falls... Had you just left.]] Imagine... what... ''[eyes close]''
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* The first chapter already has people upset, with the twins struggling to get used to the boredom of Piedmont and their parents always fighting not helping anything. Then we fast-forward three years to see Dipper living with their mom and Mabel with their dad, the twins having grown apart in the time since their parents' divorce. ''Then'' the call comes in that their Grunkle Stan died the night before.
** The twins, Soos and Wendy attend his wake, Mabel's belief in Stan not being dead causing her to open his casket and see his unmoving body, making her break down and run out of the funeral home.
* After the twins' fight in episode 5 (which is sad in and of itself), Dipper admits just how hard it had been on him going back to Piedmont after the first summer- the few people he had tried to tell about the monsters and everything had thought he was going crazy, and after his parents got divorced, he lost Mabel, the only person he could talk to about everything. He says that he's had more fun in the past week-ish that he had in the past three years, and he doesn't want to leave even though he knows he should.
* Mabel performs a HeroicSacrifice to beat the dragon in Strongholds and Serpents, completing the action just as Dipper opens his eyes to see her start to plummet hundreds of feet. He attempts a spell to save her but it does not reach her in time to prevent her from hitting the ground.
-->'''Dipper:''' No, you don't get to die like that. Not in a game I told you to play that you're not even interested in! You're going to find some stupid boyfriend somewhere that I'll actually like, and you'll get married like you wanted to, and then- ''[Wendy tries to calm him down]'' And then I'll be an uncle! I'll probably just then have someone special, and you'll tease me about it for being slow and bad with girls, like you always do! Right? You love teasing me! ''[Wendy again tries to calm him down]'' NO! She gets to tease me again! SHE'S GOING TO GET UP AND TEASE ME LIKE SHE ALWAYS DOES! ''[Wendy finally gets through to him and he collapses.]''
** They go into Hell itself to get Mabel back, but hell is Bill's domain, allowing him to possess Mabel, Soos, and Wendy and make them all attack Dipper. Dipper is able to stall Bill from possessing him long enough to tell Wendy that [[OffWithHisHead she can end Bill once and for all,]] admitting his returned feelings for her before she tearfully brings her ax up to do what needs to be done.
* The New Circuit and The Town That Time Forgot:
** After discovering Blubs and Durland are both robots, the twins agree that they can't trust anyone else with the blue-cylinder mystery, causing Dipper to push Wendy away when she offers to help.
*** Very briefly after the discovery of Blubs and Durland, the twins start trying to plan visits with each other when they go back to California, but with Dipper's job and Mabel's training, they realize that they would only be able to see each other once a week, if that.
** Then, assuming there's some kind of takeover going on, the twins start trying to test some theories when they accidentally [[ProperlyParanoid zap Soos and then Stan with the cylinders,]] revealing that [[ParanoiaFuel EVERYONE in town has been a robot the entire time.]] While they wait for something to happen, they question whether the real people are even still alive, but they have hope until...
** The Alien creators of the robots return and the twins sneak onto the ship, making "friends" with one of the Aliens, who only has time to say that the residents of Gravity Falls no longer exist before the twins are arrested by other Aliens.
*** Following both of the above scenes, each time the twins (mostly Dipper) contemplate what would have happened had they left town right after they got Grunkle Stan back, Dipper drowning in the thought that everything would have been better had he not chosen that they should spend two weeks in town.
** The real story of what happened to the people of Gravity Falls: The Aliens detected chrono-energy caused by the Portal, and the twins' Alien friend Uki-Dohth suggested putting the town in a chrono-stasis (time-lock) while they investigated, but the freezing technology was messed up because of the chrono-energy, removing the people of the town from time and existence. No matter how much time passes, the effects of the Portal will always be felt.
** Uki-Dohth, or Yuki as Mabel calls him, almost doesn't help the twins when an enemy Alien race attacks, but he does so to fix his mistake. During a fight, the helmet of his spacesuit cracks, exposing him to Earth's atmosphere. His species is able to adapt to other atmospheres, so he survives, but he is unable to return to his home planet with the rest of his species, leaving him stuck on Earth.
* When she first appears, it seems as if Pacifica has returned to her AlphaBitch nature, but as time goes on, we find out just how bad her life had become following the twins' first summer, forcing her to continue to act as if she's little-miss-perfect just to survive her parents, mostly her dad, hounding her.
* Robbie. From Zander's story about how he joined the band, to him admitting that he was jealous of how easily Dipper became friends with Wendy, it's clear that Robbie has had a hard life since what happened three years ago.
** Dipper tries to talk to Robbie again after they make up but overhears Zander saying his goodbyes and hugging the rest of the band after he surprises everyone by announcing his retirement at the end of the concert.
* Part 2 of Ashes in the Sky, starting with Pacifica helping everyone get the dying Phoenix out of the Mansion before her parents can kill it, or the mob led by Manly Dan arrives to take it, actions which we eventually find out got her kicked out of the Mansion.
** As awesome as it is to see Arline, Stan, Yuki, Grenda and Zander fight a mob to help protect the Phoenix, and Soos stop anyone who gets through the five of them, the twins and Wendy eventually realize that they are fighting not a mindless mob, but citizens of the town, people who (mostly) just want everything to return to normal, the three of them seriously considering handing over the Phoenix and admitting defeat before things get more out of hand than they already are.
** The death of the last Phoenix, not at the hands of Manly Dan, or the Northwests, or any one person, but by the bird's instincts. It crashed because of a storm, and the water has been killing it slowly every time it goes outside. Then it sees the flaming torches held by members of the mob and jumps out of the window to get to the fire... and is struck by pouring rain, killing it and cooling its ashes before anyone has a chance to do anything to save it. Between Manly Dan collapsing at the pile of ashes to Jess and Jace's tearful reaction to Wendy breaking down in tears, everyone is having a hard time convincing themselves that their survival outweighs the extinction of a species.
* A Summerween Carol is just as saddening as it's source material, if not more so:
** Past: Stan desperately tries to convince the Spirit, who has taken on Mabel's form, to not reminding him about how Summerween was created, but Mabel does so anyway, showing Stan, Ford and [=McGucket=] stressed out and fighting after dealing with the gnomes the first time. They all say they need to blow off steam, the twins instantly deciding to screw calendars and scare the daylights out of people in town with awesome costumes... all as Stan tries to ignore the entire scene in front of him and move on from the pain.
** Present: The Spirit, who looks like Soos, shows Stan the twins talking to Yuki about how Summerween works and how Stan is being a "jerk-nosed-porcupine butt"... and Yuki defends him, no matter how much the twins tell Yuki to vent and Stan says he doesn't deserve Yuki's, or anyone's, respect/faith/trust/admiration/whatever else there might be.
** Future... holy lord, the future.
*** Stan sees a warn-torn Gravity Falls, trees moving as Goblins run around town and try to stop them, the sky crackling with electricity and a battle evidently being fought on the hill under Northwest Manor. Although the faceless Spirit doesn't speak, Stan is able to piece together clues as to how the war began- the Portal was reactivated.
*** Stan sees a beaten-down Mabel apparently leading a group of survivors by the Northwest Manor, but the only other familiar faces are Pacifica and Toby, Mabel talking as if Dipper isn't there. Stan demands to know why Mabel is acting like her brother is gone, the Spirit transporting them to what is left of the Mystery Manor, the building now a pile of rubble in the cracked earth, the only thing intact being three graves labeled Soos, Dipper, and Stan.
*** Wendy runs out of the trees but a figure leaps into the air and comes crashing down on her, Yuki's foot pinning her to the ground as his partner, the Warlock, comes out as well. Stan tries and fails to stop what comes next- the Warlock throwing one ball of blackflame at the ruins of the Manor, making Wendy watch as it gets destroyed before he hits and kills her with a second ball of blackflame. The Warlock leaves, Yuki taking a second to say some cruel last words to the graves before throwing all three wooden grave markers into the flames.
** After Stan promises to change and the six-fingered Spirit sends him back to the present, Stan announces everything in the gift shop as half-off. Soos becomes deadly serious and asks Stan what his brother's name is, the two of them at some point having established this as a code for making sure Stan hasn't been replaced by a monster or something. On the surface it's just Soos following his boss' orders, but when you realize that Soos thinks the only reason Stan, the man he later quotes as being '' "[his] second father that is greater than the first" '', would give deals for no apparent reason is that he's somehow not Stan...
* Stan admitting defeat to the two kids who heckled him on Summerween in 2012... until Arline jumps in. Then the two of them, exhausted, admit their secrets to each other- Arline about her mission in town, Stan about him feeling jealous of her relationship with the twins. Seeing Stan admit defeat and being insecure, the latter probably having something to do with Yuki helping the twins earlier as well... he cares more than people think.
* The story about how Wendy became a Wraith, which gets fleshed out in the Halloween special: Robbie and Tambry got in a fight the Halloween after the twins left and broke up. Later that night, Wendy was walking down the street when Robbie started driving next to her, begging her to help him get Tambry back. Robbie tried to turn a corner without looking and his van was hit by her Dad's truck, the vehicles then hitting her and killing her on the scene. Then she woke up in the morgue, Robbie standing over her with a spellbook in hand, apparently several days after her death... which very few people know about, as her Dad's freak out following the event was the only thing the newspapers posted, not what happened to her.
** Then what comes afterward, with Wendy unable to eat, drink or sleep even though she wants to. And the few people who know she's dead- her family and friends- don't know about what Robbie did to her, meaning she had to leave town to avoid potentially awkward questions. She went to Portland for the rest of the school year, then came back with the intent to leave forever until she found out Soos and Stan apparently hadn't heard anything, so she was able to hang around the Shack/Manor over the summer and with the twins... until now, when they have found out that she is no better than the monsters they hunt and tells them to run away from her.
*** After they run away, Mabel admits to Dipper that she's scared of all kinds of undead after being possessed by the ghosts in the Dusk 2 Dawn, Wendy now included in the umbrella of 'undead=evil,' Dipper admitting that the undead are the most dangerous creatures they have encountered although he insists on doing something to fix the one mystery he couldn't solve.
* A Djinn comes to town offering cure-all's in exchange for a valued possession- Journal 3. Throughout the entire episode, Dipper debates if the Journal, the last connection they have to Ford, is worth getting a cure for Wendy. Realizing that the Journal has become outdated and he could probably survive without it, he decides that it is worth it, and he gives the Journal to the Djinn... only to be told that the pill can't revive the dead in any sense. Later, after his potential deal with Bill falls through, Dipper stares at the Journal and wonders if it's even worth keeping after what just happened. Seeing Dipper willingly give up his most important thing in the world to save his most important person in the world, only for it to not work... ugh.
* The War. The last six episodes of Season Two, from the build up in After the Shadows to the bitter end in Winds of Change... put your most comfortable sweater on because you will want to disappear into Sweater Town.
** The first thing that happens is a cave-in which causes the junkyard to collapse on top of Omir Steindorf, the twins and Zander barely escaping with their lives, Dipper raging about Omir being killed by the Warlock and threatening to kill him the next time they meet.
** Everyone's reactions to the discovery of Yuki meeting with the Warlock:
*** Soos and Wendy (and Arline) found out together, Wendy becoming quiet and sombre, Soos tearing up and the news. We don't get Arline's reaction until much later, [[spoiler: when she accuses Zander of being the suspicious one instead of Yuki.]]
*** Zander, who first made the discovery with the twins, suggests asking Yuki before jumping to conclusions, but he and the twins all know there is no mistaking the fact that Yuki had met with the Warlock repeatedly. Later, [[spoiler: in his secret StringTheory room,]] he even comments that Yuki working with the Warlock isn't what he expected. Also, he is the one who tells Pacifica about what happened.
*** The twins- Mabel is in denial, Dipper is furious, especially when he sees that Yuki took his notes for curing Wendy. He attacks Yuki, taking Mabel, Soos and Stan to pull him away. After Stan kicks Yuki out, Dipper tells him to leave, but Yuki begs Mabel to trust him. Mabel's response is to turn away, sealing his fate.
*** Stan. For the record, the first thing he does is defend Yuki, and it's not until Yuki doesn't deny the accusations that he becomes coldly furious. Even then, he gives Yuki three chances to tell them everything and let everyone put it behind them. It's not until Yuki says he can't go back on the promise that Stan's rage becomes apparent, literally kicking Yuki out of the Manor and yelling at him-
--->'''Stan:''' I let you stay in my home, in my ''brother's'' home, with the understanding that you'd be on our side when this sort of thing happened. Instead, you went ahead and made a deal with the BAD GUY! You can forget about ever coming back here. In fact- ''[throws Yuki's belongings outside]'' Take it all! I don't want anything that reminds me I let a backstabber like you in this house! That's... that's the least I can do. You deserve so much more. Endangering my kids like that. You don't know what being human means, not by a long shot." ''[slams door as he goes back inside]''
*** Even Yuki himself is upset, begging everyone to understand that he didn't mean to hurt them and that what happened today wasn't his fault, but still refusing to tell them everything, meaning no one believes him, except for Pacifica, who we eventually find out took him into the Mansion after he got kicked out.
** [[TonightSomeoneDies Part 2 of Fires of Hate.]] Dipper gets the revenge he talked about after the cave-in, punching and kicking the Warlock for everything he has done to them and their family/friends, and it eventually turns into Dipper letting out the emotions left behind from what happened three years ago. Then Dipper misses a punch, and the next thing anyone knows is that the Warlock has fried his hands with blackflame. The pain makes Dipper's brain shutdown, unable to do anything as the Warlock prepares to kill him with another ball of- Yuki shows up. He begs Dipper to leave if he can and refuses to move out of the way when the Warlock threatens to kill them both. The first ball hits Yuki in the shoulder. The second hits him in the stomach. The Warlock hurls more and more blackflame at Yuki, Dipper only able to watch as his friend gets burned to a crisp... and for the first time since they've met, become furious. [[MartialPacifist Yuki punches the Warlock clear across the room]] and walks directly to him despite being hit by a continuous stream of blackflame. [[ThouShaltNotKill He grab the Warlock's throat with one hand and uses the other hand to tie a chain around his neck, throwing the Warlock off the edge of a pit]] before collapsing himself, Dipper realizing that they have lost.
** All of Cleansing Rain and Part 1 of Broken Earth, starting with Shandra's news report. Between the collapsed junkyard, the buildings destroyed by the battle with the Golem (making a number of people loose their homes), and the money lost because of failed events, Shandra is stunned when she finds out that "...people are starting to wonder if Gravity Falls is going to remain on the map for much longer..." is not melodramatic- the survival of the town is seriously being questioned. [[DarkestHour Then the power goes out.]]
*** Stan's reaction to what happened to Yuki, the twins describing the way he looks and acts as being similar to his reaction three years ago. He is barely able to choke out that he doesn't think Yuki will be around much longer, then the next time we see him, he has decided to close down the Manor for good, not wanting to go through another loss like that of Ford or Yuki again. The loss of Yuki is equal to that of loosing his brother. Wow.
*** Yuki's DeathbedConfession about why he worked with the Warlock- to protect the twins. In exchange for Yuki helping the Warlock with a side project, the Warlock promised to not attack the twins unless his life was in danger... and it would have worked if Yuki had just told the twins what was going on. He apologizes for being naive but says that it was worth it to protect his family from the harshness of the world. He starts falling asleep, Pacifica and the twins desperate to find a way to still be there when he wakes up from the at least 80-year healing coma he is about to go into. He tells Pacifica to keep learning from Zander and to be better than her parents, agrees to another chess match with Dipper if he's still around when he wakes up, and tells Mabel that she taught him more about being human than anyone else did.
--->'''[[FamousLastWords Yuki:]]''' I'm lucky, so lucky for this. For you all. [[CallBack Imagine what... what would have happened if you two had never stayed in Gravity Falls... Had you just left.]] Imagine... what... ''[eyes close]''
*** The two big arguments of the chapters, the first between Mabel and Arline, the former upset about everyone keeping secrets and messing everything up. Then she finds out that Arline told Stan about her real mission in exchange for seeing the Portal, while the twins were left completely in the dark on both accounts, Mabel unable to trust Arline any more because of all the secrets. The second argument is between Wendy and Dipper, the former trying to convince him that he'll be able to move past the loss of his hands. Dipper misinterprets this as he should be grateful and the argument quickly turns to who's curse is better or worse, Dipper culminating his rant into telling Wendy to keep her self pity to herself, realizing much too late the line he just crossed.
*** Just after Wendy and Dipper make up, Zander shows up with Magenta close behind him, everyone instantly realizing something is wrong because Zander, the man they all know as a free spirit similar to Mabel, is not happy or smiling and appears tense. He says that Pacifica's parents think he kidnapped her and literally pulls Pacifica away from Yuki to get her parents off his back so he can leave town as soon as she's safe. Mabel begs him to not give up despite how desperate the situation looks, but he still leaves. Probably the most hopeful person in the story after Mabel herself thinks there is nothing that can be done.
*** Dipper mentions the Guardsman maybe being able to save Yuki, but before any of them can head into the woods, something in town explodes, making them loose their last chance of getting Yuki back. Then they find out the Warlock survived being hung, making Yuki's sacrifice worthless.
** Omir attacks the Manor, promising to revive Yuki in exchange for Stan taking him to the Portal. It's not until Omir has Wendy trapped that Stan agrees, but it doesn't stop him from backing Soos when he attacks Omir again. Then Soos is trapped as well, Stan tearfully and desperately agreeing to Omir's deal, not wanting to loose another employee and go through the pain of loosing Ford and Yuki again.
** TheReveal that everything Omir has been doing in an attempt to bring his lost love Haddiya back was actually all just a trick by Bill and Haddiya has been dead all along. While Omir was technically evil, he was at least a decent and fair person, and seeing him enter a BSOD is heart-wrenching.
** The Portal starts exploding, eating away at reality itself to keep itself active. So what does everyone do to stop the end of the world? Stan gives Soos the keys to his El Diablo and tells him to keep Wendy and the twins safe, Arline quickly shoving everyone into the elevator and sending them upstairs while she, Stan and Omir feed energy into the Portal to delay the explosion for as long as they can...
*** And the Portal explodes anyway, taking the three of them as well as half the Manor with it almost instantly. Soos, Wendy and the twins don't even have time to get Yuki into one of the cars before they are forced to drive away from the explosion. After the explosion stops, the four survivors figure out just how bad it was- Gravity Falls no longer exists, the explosion being a reality explosion removing the town and people from ever existing. Stan, Yuki, Arline, Wendy's family and friends and her mother's resting spot- it's all gone. Even the Guardsman says nothing can be done today.
* Two moments in The Parents Traps, the first being the twins wondering if people in their family naturally tend to drift apart and wondering if that will happen to them as well. The second thing is us FINALLY getting the full story about what happened with Ford three years ago- While he was in the Portal, he made a second deal with Bill that allowed Bill to possess him even when he came back into the real world. Ford wasn't strong enough to fight Bill, so in order to save Stan and the world, the twins had to throw the possessed Ford back into the Portal.
* While they're all traveling across the country, some of the places they stop at remind them of Gravity Falls. A Gift Shop in Home on the Range reminds Soos about the one in the Manor, and the entire city of Chicago reminds Wendy of her family- tough, strong, and always ready for a fight.
* At first it seems like Waddles will be forced to say goodbye to his girlfriend Mina again, but he doesn't have too... because Mabel decides traveling with them is too dangerous for him and opts to leave him with Mr. Gullian, Mina's owner.
* The entire situation on Gracey Island- Edward's wife got sick shortly after giving birth to Constance, Edward spending ten years trying to keep his wife alive so his daughter could grow up with a mother, but his wife died anyway. He started working to provide for himself and Constance, not realizing he was abandoning her in the process to think true love could come from thin air. Then she got married and killed her husband after realizing it wasn't true love, repeating the process with her next several husbands. After she and her father got into a shouting match during a party, she poisoned all the party guests (nearly 1000 of them) and herself, her father hanging himself after watching everyone die, trapping everyone on the island for ''the past 150 years!''
* Stan talking to Ford/The Portal after telling Arline the story of what happened three years ago.
-->'''Stan:''' ''[with his hand on the Portal]'' Hey brother, still can't hear me, right? You know, I still don't blame you, right? I really don't, bro. I messed up for you once, just once, and look what it did. Made you obsessed with proving to people you were worth something, something truly great. ''[walks away from Portal, turns around at door]'' You... you never had to prove a thing to me. ''[Turns out lights and leaves]''
* Two moments in Fight or Flight, the first when the twins find out that Jess and Jace have begun being attacked purely because they have met the twins before. The second moment is when Jess reveals her feelings to an unconscious Dipper after he has both been hit by a tranq dart and fallen into a large boiling vat. The latter really did stun him for a bit, but because the tranq dart hit the Journal instead of him, he heard her confession, the similarities to his confession to 'Wendy' in Into the Bunker not lost on anyone.
* Through most of Season Three, Soos has begun to feel useless, but it's not until Alberta Jeffreys calls him out for being fat and having to rely on Wendy and the twins to protect him that he decides to take action- by agreeing to a deal offered by Bill's sister Kelly to change one event in his life and rewrite the entire timeline.
** As great as the alternate timeline first appears to be, (the town is back, his grandmother is still alive, he's the town's go-to fix-it man, Wendy is alive, and the twins are excelling at academics and the Paths) Soos eventually discovers that the event that changed was that [[spoiler: he never worked at the Shack]], and things quickly start going south from there. Wendy has started smoking and drinking, and the twins got sent home after the trouble with Gideon, growing apart just like they did in the original timeline. Soos then goes to the Shack and discovers Omir and the Warlock both working there under Stan's command... except Stan has been possessed by Bill. This all culminates in a standoff in front of the Portal, Bill holding a knife to Stan's neck, threatening to kill Stan if Soos attacks. Stan's last orders to protect the twins allows Soos to let Bill stab Stan in the chest, but when the knife turned out to be fake anyway, Soos was able to lift Bill up and throw him to the opening of the Portal.
* When the gang goes to Niagara University, Mabel admits to Dipper that she's scared things are going to get worse for them before they actually save the world, then she says she's concerned about them being able to have a normal life if they are saving the world every summer. She then admits that she's really just scared that they will grow apart if they have to go back to normal life with their parents, and Dipper is unable to assure her that they will be able to make it work.
* People have started dying, actually dying, now. The Jersey Devil first killed a number of the Warlock's cultists before dying himself. Then the twins meet up with Montana Jeffreys, who happens to be the Warlock's hero. A lot of serious stuff goes down, and it culminates in the Warlock killing Montana, Montana's two dogs, and over a dozen police and civilians. Not to mention an undisclosed number of fatalities from the Paths fighting in Mississippi and a fire started during the encounter with the Devil taking several lives, it's no wonder everyone becomes slightly depressed after Montana is killed.
** The twins, Soos and Wendy attend his wake, Mabel's belief in Stan not being dead causing her to open his casket and see his unmoving body, making her break down and run out of the funeral home.
* After the twins' fight in episode 5 (which is sad in and of itself), Dipper admits just how hard it had been on him going back to Piedmont after the first summer- the few people he had tried to tell about the monsters and everything had thought he was going crazy, and after his parents got divorced, he lost Mabel, the only person he could talk to about everything. He says that he's had more fun in the past week-ish that he had in the past three years, and he doesn't want to leave even though he knows he should.
* Mabel performs a HeroicSacrifice to beat the dragon in Strongholds and Serpents, completing the action just as Dipper opens his eyes to see her start to plummet hundreds of feet. He attempts a spell to save her but it does not reach her in time to prevent her from hitting the ground.
-->'''Dipper:''' No, you don't get to die like that. Not in a game I told you to play that you're not even interested in! You're going to find some stupid boyfriend somewhere that I'll actually like, and you'll get married like you wanted to, and then- ''[Wendy tries to calm him down]'' And then I'll be an uncle! I'll probably just then have someone special, and you'll tease me about it for being slow and bad with girls, like you always do! Right? You love teasing me! ''[Wendy again tries to calm him down]'' NO! She gets to tease me again! SHE'S GOING TO GET UP AND TEASE ME LIKE SHE ALWAYS DOES! ''[Wendy finally gets through to him and he collapses.]''
** They go into Hell itself to get Mabel back, but hell is Bill's domain, allowing him to possess Mabel, Soos, and Wendy and make them all attack Dipper. Dipper is able to stall Bill from possessing him long enough to tell Wendy that [[OffWithHisHead she can end Bill once and for all,]] admitting his returned feelings for her before she tearfully brings her ax up to do what needs to be done.
* The New Circuit and The Town That Time Forgot:
** After discovering Blubs and Durland are both robots, the twins agree that they can't trust anyone else with the blue-cylinder mystery, causing Dipper to push Wendy away when she offers to help.
*** Very briefly after the discovery of Blubs and Durland, the twins start trying to plan visits with each other when they go back to California, but with Dipper's job and Mabel's training, they realize that they would only be able to see each other once a week, if that.
** Then, assuming there's some kind of takeover going on, the twins start trying to test some theories when they accidentally [[ProperlyParanoid zap Soos and then Stan with the cylinders,]] revealing that [[ParanoiaFuel EVERYONE in town has been a robot the entire time.]] While they wait for something to happen, they question whether the real people are even still alive, but they have hope until...
** The Alien creators of the robots return and the twins sneak onto the ship, making "friends" with one of the Aliens, who only has time to say that the residents of Gravity Falls no longer exist before the twins are arrested by other Aliens.
*** Following both of the above scenes, each time the twins (mostly Dipper) contemplate what would have happened had they left town right after they got Grunkle Stan back, Dipper drowning in the thought that everything would have been better had he not chosen that they should spend two weeks in town.
** The real story of what happened to the people of Gravity Falls: The Aliens detected chrono-energy caused by the Portal, and the twins' Alien friend Uki-Dohth suggested putting the town in a chrono-stasis (time-lock) while they investigated, but the freezing technology was messed up because of the chrono-energy, removing the people of the town from time and existence. No matter how much time passes, the effects of the Portal will always be felt.
** Uki-Dohth, or Yuki as Mabel calls him, almost doesn't help the twins when an enemy Alien race attacks, but he does so to fix his mistake. During a fight, the helmet of his spacesuit cracks, exposing him to Earth's atmosphere. His species is able to adapt to other atmospheres, so he survives, but he is unable to return to his home planet with the rest of his species, leaving him stuck on Earth.
* When she first appears, it seems as if Pacifica has returned to her AlphaBitch nature, but as time goes on, we find out just how bad her life had become following the twins' first summer, forcing her to continue to act as if she's little-miss-perfect just to survive her parents, mostly her dad, hounding her.
* Robbie. From Zander's story about how he joined the band, to him admitting that he was jealous of how easily Dipper became friends with Wendy, it's clear that Robbie has had a hard life since what happened three years ago.
** Dipper tries to talk to Robbie again after they make up but overhears Zander saying his goodbyes and hugging the rest of the band after he surprises everyone by announcing his retirement at the end of the concert.
* Part 2 of Ashes in the Sky, starting with Pacifica helping everyone get the dying Phoenix out of the Mansion before her parents can kill it, or the mob led by Manly Dan arrives to take it, actions which we eventually find out got her kicked out of the Mansion.
** As awesome as it is to see Arline, Stan, Yuki, Grenda and Zander fight a mob to help protect the Phoenix, and Soos stop anyone who gets through the five of them, the twins and Wendy eventually realize that they are fighting not a mindless mob, but citizens of the town, people who (mostly) just want everything to return to normal, the three of them seriously considering handing over the Phoenix and admitting defeat before things get more out of hand than they already are.
** The death of the last Phoenix, not at the hands of Manly Dan, or the Northwests, or any one person, but by the bird's instincts. It crashed because of a storm, and the water has been killing it slowly every time it goes outside. Then it sees the flaming torches held by members of the mob and jumps out of the window to get to the fire... and is struck by pouring rain, killing it and cooling its ashes before anyone has a chance to do anything to save it. Between Manly Dan collapsing at the pile of ashes to Jess and Jace's tearful reaction to Wendy breaking down in tears, everyone is having a hard time convincing themselves that their survival outweighs the extinction of a species.
* A Summerween Carol is just as saddening as it's source material, if not more so:
** Past: Stan desperately tries to convince the Spirit, who has taken on Mabel's form, to not reminding him about how Summerween was created, but Mabel does so anyway, showing Stan, Ford and [=McGucket=] stressed out and fighting after dealing with the gnomes the first time. They all say they need to blow off steam, the twins instantly deciding to screw calendars and scare the daylights out of people in town with awesome costumes... all as Stan tries to ignore the entire scene in front of him and move on from the pain.
** Present: The Spirit, who looks like Soos, shows Stan the twins talking to Yuki about how Summerween works and how Stan is being a "jerk-nosed-porcupine butt"... and Yuki defends him, no matter how much the twins tell Yuki to vent and Stan says he doesn't deserve Yuki's, or anyone's, respect/faith/trust/admiration/whatever else there might be.
** Future... holy lord, the future.
*** Stan sees a warn-torn Gravity Falls, trees moving as Goblins run around town and try to stop them, the sky crackling with electricity and a battle evidently being fought on the hill under Northwest Manor. Although the faceless Spirit doesn't speak, Stan is able to piece together clues as to how the war began- the Portal was reactivated.
*** Stan sees a beaten-down Mabel apparently leading a group of survivors by the Northwest Manor, but the only other familiar faces are Pacifica and Toby, Mabel talking as if Dipper isn't there. Stan demands to know why Mabel is acting like her brother is gone, the Spirit transporting them to what is left of the Mystery Manor, the building now a pile of rubble in the cracked earth, the only thing intact being three graves labeled Soos, Dipper, and Stan.
*** Wendy runs out of the trees but a figure leaps into the air and comes crashing down on her, Yuki's foot pinning her to the ground as his partner, the Warlock, comes out as well. Stan tries and fails to stop what comes next- the Warlock throwing one ball of blackflame at the ruins of the Manor, making Wendy watch as it gets destroyed before he hits and kills her with a second ball of blackflame. The Warlock leaves, Yuki taking a second to say some cruel last words to the graves before throwing all three wooden grave markers into the flames.
** After Stan promises to change and the six-fingered Spirit sends him back to the present, Stan announces everything in the gift shop as half-off. Soos becomes deadly serious and asks Stan what his brother's name is, the two of them at some point having established this as a code for making sure Stan hasn't been replaced by a monster or something. On the surface it's just Soos following his boss' orders, but when you realize that Soos thinks the only reason Stan, the man he later quotes as being '' "[his] second father that is greater than the first" '', would give deals for no apparent reason is that he's somehow not Stan...
* Stan admitting defeat to the two kids who heckled him on Summerween in 2012... until Arline jumps in. Then the two of them, exhausted, admit their secrets to each other- Arline about her mission in town, Stan about him feeling jealous of her relationship with the twins. Seeing Stan admit defeat and being insecure, the latter probably having something to do with Yuki helping the twins earlier as well... he cares more than people think.
* The story about how Wendy became a Wraith, which gets fleshed out in the Halloween special: Robbie and Tambry got in a fight the Halloween after the twins left and broke up. Later that night, Wendy was walking down the street when Robbie started driving next to her, begging her to help him get Tambry back. Robbie tried to turn a corner without looking and his van was hit by her Dad's truck, the vehicles then hitting her and killing her on the scene. Then she woke up in the morgue, Robbie standing over her with a spellbook in hand, apparently several days after her death... which very few people know about, as her Dad's freak out following the event was the only thing the newspapers posted, not what happened to her.
** Then what comes afterward, with Wendy unable to eat, drink or sleep even though she wants to. And the few people who know she's dead- her family and friends- don't know about what Robbie did to her, meaning she had to leave town to avoid potentially awkward questions. She went to Portland for the rest of the school year, then came back with the intent to leave forever until she found out Soos and Stan apparently hadn't heard anything, so she was able to hang around the Shack/Manor over the summer and with the twins... until now, when they have found out that she is no better than the monsters they hunt and tells them to run away from her.
*** After they run away, Mabel admits to Dipper that she's scared of all kinds of undead after being possessed by the ghosts in the Dusk 2 Dawn, Wendy now included in the umbrella of 'undead=evil,' Dipper admitting that the undead are the most dangerous creatures they have encountered although he insists on doing something to fix the one mystery he couldn't solve.
* A Djinn comes to town offering cure-all's in exchange for a valued possession- Journal 3. Throughout the entire episode, Dipper debates if the Journal, the last connection they have to Ford, is worth getting a cure for Wendy. Realizing that the Journal has become outdated and he could probably survive without it, he decides that it is worth it, and he gives the Journal to the Djinn... only to be told that the pill can't revive the dead in any sense. Later, after his potential deal with Bill falls through, Dipper stares at the Journal and wonders if it's even worth keeping after what just happened. Seeing Dipper willingly give up his most important thing in the world to save his most important person in the world, only for it to not work... ugh.
* The War. The last six episodes of Season Two, from the build up in After the Shadows to the bitter end in Winds of Change... put your most comfortable sweater on because you will want to disappear into Sweater Town.
** The first thing that happens is a cave-in which causes the junkyard to collapse on top of Omir Steindorf, the twins and Zander barely escaping with their lives, Dipper raging about Omir being killed by the Warlock and threatening to kill him the next time they meet.
** Everyone's reactions to the discovery of Yuki meeting with the Warlock:
*** Soos and Wendy (and Arline) found out together, Wendy becoming quiet and sombre, Soos tearing up and the news. We don't get Arline's reaction until much later, [[spoiler: when she accuses Zander of being the suspicious one instead of Yuki.]]
*** Zander, who first made the discovery with the twins, suggests asking Yuki before jumping to conclusions, but he and the twins all know there is no mistaking the fact that Yuki had met with the Warlock repeatedly. Later, [[spoiler: in his secret StringTheory room,]] he even comments that Yuki working with the Warlock isn't what he expected. Also, he is the one who tells Pacifica about what happened.
*** The twins- Mabel is in denial, Dipper is furious, especially when he sees that Yuki took his notes for curing Wendy. He attacks Yuki, taking Mabel, Soos and Stan to pull him away. After Stan kicks Yuki out, Dipper tells him to leave, but Yuki begs Mabel to trust him. Mabel's response is to turn away, sealing his fate.
*** Stan. For the record, the first thing he does is defend Yuki, and it's not until Yuki doesn't deny the accusations that he becomes coldly furious. Even then, he gives Yuki three chances to tell them everything and let everyone put it behind them. It's not until Yuki says he can't go back on the promise that Stan's rage becomes apparent, literally kicking Yuki out of the Manor and yelling at him-
--->'''Stan:''' I let you stay in my home, in my ''brother's'' home, with the understanding that you'd be on our side when this sort of thing happened. Instead, you went ahead and made a deal with the BAD GUY! You can forget about ever coming back here. In fact- ''[throws Yuki's belongings outside]'' Take it all! I don't want anything that reminds me I let a backstabber like you in this house! That's... that's the least I can do. You deserve so much more. Endangering my kids like that. You don't know what being human means, not by a long shot." ''[slams door as he goes back inside]''
*** Even Yuki himself is upset, begging everyone to understand that he didn't mean to hurt them and that what happened today wasn't his fault, but still refusing to tell them everything, meaning no one believes him, except for Pacifica, who we eventually find out took him into the Mansion after he got kicked out.
** [[TonightSomeoneDies Part 2 of Fires of Hate.]] Dipper gets the revenge he talked about after the cave-in, punching and kicking the Warlock for everything he has done to them and their family/friends, and it eventually turns into Dipper letting out the emotions left behind from what happened three years ago. Then Dipper misses a punch, and the next thing anyone knows is that the Warlock has fried his hands with blackflame. The pain makes Dipper's brain shutdown, unable to do anything as the Warlock prepares to kill him with another ball of- Yuki shows up. He begs Dipper to leave if he can and refuses to move out of the way when the Warlock threatens to kill them both. The first ball hits Yuki in the shoulder. The second hits him in the stomach. The Warlock hurls more and more blackflame at Yuki, Dipper only able to watch as his friend gets burned to a crisp... and for the first time since they've met, become furious. [[MartialPacifist Yuki punches the Warlock clear across the room]] and walks directly to him despite being hit by a continuous stream of blackflame. [[ThouShaltNotKill He grab the Warlock's throat with one hand and uses the other hand to tie a chain around his neck, throwing the Warlock off the edge of a pit]] before collapsing himself, Dipper realizing that they have lost.
** All of Cleansing Rain and Part 1 of Broken Earth, starting with Shandra's news report. Between the collapsed junkyard, the buildings destroyed by the battle with the Golem (making a number of people loose their homes), and the money lost because of failed events, Shandra is stunned when she finds out that "...people are starting to wonder if Gravity Falls is going to remain on the map for much longer..." is not melodramatic- the survival of the town is seriously being questioned. [[DarkestHour Then the power goes out.]]
*** Stan's reaction to what happened to Yuki, the twins describing the way he looks and acts as being similar to his reaction three years ago. He is barely able to choke out that he doesn't think Yuki will be around much longer, then the next time we see him, he has decided to close down the Manor for good, not wanting to go through another loss like that of Ford or Yuki again. The loss of Yuki is equal to that of loosing his brother. Wow.
*** Yuki's DeathbedConfession about why he worked with the Warlock- to protect the twins. In exchange for Yuki helping the Warlock with a side project, the Warlock promised to not attack the twins unless his life was in danger... and it would have worked if Yuki had just told the twins what was going on. He apologizes for being naive but says that it was worth it to protect his family from the harshness of the world. He starts falling asleep, Pacifica and the twins desperate to find a way to still be there when he wakes up from the at least 80-year healing coma he is about to go into. He tells Pacifica to keep learning from Zander and to be better than her parents, agrees to another chess match with Dipper if he's still around when he wakes up, and tells Mabel that she taught him more about being human than anyone else did.
--->'''[[FamousLastWords Yuki:]]''' I'm lucky, so lucky for this. For you all. [[CallBack Imagine what... what would have happened if you two had never stayed in Gravity Falls... Had you just left.]] Imagine... what... ''[eyes close]''
*** The two big arguments of the chapters, the first between Mabel and Arline, the former upset about everyone keeping secrets and messing everything up. Then she finds out that Arline told Stan about her real mission in exchange for seeing the Portal, while the twins were left completely in the dark on both accounts, Mabel unable to trust Arline any more because of all the secrets. The second argument is between Wendy and Dipper, the former trying to convince him that he'll be able to move past the loss of his hands. Dipper misinterprets this as he should be grateful and the argument quickly turns to who's curse is better or worse, Dipper culminating his rant into telling Wendy to keep her self pity to herself, realizing much too late the line he just crossed.
*** Just after Wendy and Dipper make up, Zander shows up with Magenta close behind him, everyone instantly realizing something is wrong because Zander, the man they all know as a free spirit similar to Mabel, is not happy or smiling and appears tense. He says that Pacifica's parents think he kidnapped her and literally pulls Pacifica away from Yuki to get her parents off his back so he can leave town as soon as she's safe. Mabel begs him to not give up despite how desperate the situation looks, but he still leaves. Probably the most hopeful person in the story after Mabel herself thinks there is nothing that can be done.
*** Dipper mentions the Guardsman maybe being able to save Yuki, but before any of them can head into the woods, something in town explodes, making them loose their last chance of getting Yuki back. Then they find out the Warlock survived being hung, making Yuki's sacrifice worthless.
** Omir attacks the Manor, promising to revive Yuki in exchange for Stan taking him to the Portal. It's not until Omir has Wendy trapped that Stan agrees, but it doesn't stop him from backing Soos when he attacks Omir again. Then Soos is trapped as well, Stan tearfully and desperately agreeing to Omir's deal, not wanting to loose another employee and go through the pain of loosing Ford and Yuki again.
** TheReveal that everything Omir has been doing in an attempt to bring his lost love Haddiya back was actually all just a trick by Bill and Haddiya has been dead all along. While Omir was technically evil, he was at least a decent and fair person, and seeing him enter a BSOD is heart-wrenching.
** The Portal starts exploding, eating away at reality itself to keep itself active. So what does everyone do to stop the end of the world? Stan gives Soos the keys to his El Diablo and tells him to keep Wendy and the twins safe, Arline quickly shoving everyone into the elevator and sending them upstairs while she, Stan and Omir feed energy into the Portal to delay the explosion for as long as they can...
*** And the Portal explodes anyway, taking the three of them as well as half the Manor with it almost instantly. Soos, Wendy and the twins don't even have time to get Yuki into one of the cars before they are forced to drive away from the explosion. After the explosion stops, the four survivors figure out just how bad it was- Gravity Falls no longer exists, the explosion being a reality explosion removing the town and people from ever existing. Stan, Yuki, Arline, Wendy's family and friends and her mother's resting spot- it's all gone. Even the Guardsman says nothing can be done today.
* Two moments in The Parents Traps, the first being the twins wondering if people in their family naturally tend to drift apart and wondering if that will happen to them as well. The second thing is us FINALLY getting the full story about what happened with Ford three years ago- While he was in the Portal, he made a second deal with Bill that allowed Bill to possess him even when he came back into the real world. Ford wasn't strong enough to fight Bill, so in order to save Stan and the world, the twins had to throw the possessed Ford back into the Portal.
* While they're all traveling across the country, some of the places they stop at remind them of Gravity Falls. A Gift Shop in Home on the Range reminds Soos about the one in the Manor, and the entire city of Chicago reminds Wendy of her family- tough, strong, and always ready for a fight.
* At first it seems like Waddles will be forced to say goodbye to his girlfriend Mina again, but he doesn't have too... because Mabel decides traveling with them is too dangerous for him and opts to leave him with Mr. Gullian, Mina's owner.
* The entire situation on Gracey Island- Edward's wife got sick shortly after giving birth to Constance, Edward spending ten years trying to keep his wife alive so his daughter could grow up with a mother, but his wife died anyway. He started working to provide for himself and Constance, not realizing he was abandoning her in the process to think true love could come from thin air. Then she got married and killed her husband after realizing it wasn't true love, repeating the process with her next several husbands. After she and her father got into a shouting match during a party, she poisoned all the party guests (nearly 1000 of them) and herself, her father hanging himself after watching everyone die, trapping everyone on the island for ''the past 150 years!''
* Stan talking to Ford/The Portal after telling Arline the story of what happened three years ago.
-->'''Stan:''' ''[with his hand on the Portal]'' Hey brother, still can't hear me, right? You know, I still don't blame you, right? I really don't, bro. I messed up for you once, just once, and look what it did. Made you obsessed with proving to people you were worth something, something truly great. ''[walks away from Portal, turns around at door]'' You... you never had to prove a thing to me. ''[Turns out lights and leaves]''
* Two moments in Fight or Flight, the first when the twins find out that Jess and Jace have begun being attacked purely because they have met the twins before. The second moment is when Jess reveals her feelings to an unconscious Dipper after he has both been hit by a tranq dart and fallen into a large boiling vat. The latter really did stun him for a bit, but because the tranq dart hit the Journal instead of him, he heard her confession, the similarities to his confession to 'Wendy' in Into the Bunker not lost on anyone.
* Through most of Season Three, Soos has begun to feel useless, but it's not until Alberta Jeffreys calls him out for being fat and having to rely on Wendy and the twins to protect him that he decides to take action- by agreeing to a deal offered by Bill's sister Kelly to change one event in his life and rewrite the entire timeline.
** As great as the alternate timeline first appears to be, (the town is back, his grandmother is still alive, he's the town's go-to fix-it man, Wendy is alive, and the twins are excelling at academics and the Paths) Soos eventually discovers that the event that changed was that [[spoiler: he never worked at the Shack]], and things quickly start going south from there. Wendy has started smoking and drinking, and the twins got sent home after the trouble with Gideon, growing apart just like they did in the original timeline. Soos then goes to the Shack and discovers Omir and the Warlock both working there under Stan's command... except Stan has been possessed by Bill. This all culminates in a standoff in front of the Portal, Bill holding a knife to Stan's neck, threatening to kill Stan if Soos attacks. Stan's last orders to protect the twins allows Soos to let Bill stab Stan in the chest, but when the knife turned out to be fake anyway, Soos was able to lift Bill up and throw him to the opening of the Portal.
* When the gang goes to Niagara University, Mabel admits to Dipper that she's scared things are going to get worse for them before they actually save the world, then she says she's concerned about them being able to have a normal life if they are saving the world every summer. She then admits that she's really just scared that they will grow apart if they have to go back to normal life with their parents, and Dipper is unable to assure her that they will be able to make it work.
* People have started dying, actually dying, now. The Jersey Devil first killed a number of the Warlock's cultists before dying himself. Then the twins meet up with Montana Jeffreys, who happens to be the Warlock's hero. A lot of serious stuff goes down, and it culminates in the Warlock killing Montana, Montana's two dogs, and over a dozen police and civilians. Not to mention an undisclosed number of fatalities from the Paths fighting in Mississippi and a fire started during the encounter with the Devil taking several lives, it's no wonder everyone becomes slightly depressed after Montana is killed.
