The original idea for this story was going to be centered around Dipper and what the effects of having your soul ripped out of your body for a prolonged period of time might be, but then I got ideas about Mabel and Stan and it turned into a study of Bill's effect on all three of them. I couldn't get the original idea out of my head, so here's something a little more Dipper-centric.

The first time it happened, Dipper panicked. He'd woken up from a nightmare, one where they'd failed, Bill had won. He sat up suddenly, a yelp escaping before he clamped his hand over his mouth, and then he'd screamed in horror when he turned around to lay down and go back to sleep and his body was laying under him.

The panic hadn't faded for over a week, and he was convinced every triangle and eye he saw was about to come alive.

Then it happened again, another nightmare. This time one about the shapeshifter, Dipper hurting Wendy on accident, all of them dead in a bunker no one would ever find.
He panicked only slightly less this time, and Mabel told him she'd been having hallucinations. Seeing Mabeland all over again.

Then it happened a third time. Mabel kept hallucinating, she yelled at him to stop clicking his pen late at night and he found he no longer could.
Mabel did not speak for a week after that, except to undo it once he'd discovered what had happened.

A fourth time, in front of his parents. He ended up in the hospital after that, everyone confused as to how he'd seemingly pulled himself back from the dead.

A fifth, a sixth, a seventh.

Again and again and it hardly scared him anymore.

Finally, after two months, he tried it himself. He didn't have much luck the first time, but the next time it happened on accident he tried to focus on what it felt like to fall out of himself. He felt nothing. No cold burning like the first time and the deal, no gentle chill, no warmth, not even an absence of warmth. But then, he found he could not feel. He didn't feel his hands on his arms, couldn't feel the cold metal of his bed frame.

When he tried again he focused on the cold porcelain under his hands, the itch where his jacket made his neck just a little too warm, and pulled himself away from it.
His body fell dead (that should scare him more), and he whooped with glee.

Mabel didn't like it, but he never had trouble getting back in his body, never felt like he was fading away, so he didn't worry (he should have).

He started reaching for things with phantom limbs, arms falling limp at his side. When he turned to look at something his head didn't follow. His legs stopped being able to keep pace. He was out of sync with his own body.

He gave himself a nasty burn on accident when baking cookies over the holiday season, and still he used the hand until his mother noticed how red and raw it was. It barely hurt at all.
He broke his arm and leg falling down the stairs, and once the sharp pain that came with the sickening snap faded away, he felt fine.

He stops speaking halfway through sentences sometimes, mouth falling slack, teeth clacking loudly.

They don't return to Gravity Falls that summer. Stan and Ford are tied up somewhere dealing with supernatural something, Soos is dealing with his first summer influx of tourists, and Wendy and the other teens ended up taking an unplanned road trip.

Mabel pierces his ears in the bathroom while their parents are out, he shouldn't be trusted with his own body right now, and he doesn't feel the sting. His parents are angry but mostly just that he didn't ask, and so he brings up the idea of a small tattoo.
They tell him at the end of the school year, if his grades stay good. He gets a vine that makes a loop around his arm midway up his bicep, and he nearly cries with relief when it stings right near the end.

Mabel swears it moves sometimes when she looks at it, but he knows the sky has gone rainbow for her when that happens.

Again they don't go to Gravity Falls, and they're both starting to feel the wear of not seeing their friends (nevermind that Piedmont is dirt-boring and lonely and feels less and less like home every day compared to Gravity Falls), but they call them and video chat everyone on their birthday so it's kind of alright. They all love Dipper's new tattoo and Melody is there showing off her engagement ring (Soos makes them promise to be there for the wedding), and Candy and Grenda compliment Mabel on her improved sewing skills.

Dipper gets a part time job that summer and saves up for another tattoo, a UFO on the back of his shoulder. This one stings more, and when that fades he finds he can feel warmth again, but it's like touching someone's arm when you're wearing gloves and they're wearing a jacket. Muffled and faint. He's still out of sync.

He gets another piercing, this one in his eyebrow, and it stings. People at school start to whisper, and he can't blame them. He's been shoved into the nerd box and never bothered to try and get out of it, but he likes the piercings and tattoos for reasons other than just being able to feel the sharp sting of them.
The tattoos build up, always small since he doesn't have the money for big ones, but he has at least half a dozen when winter rolls around again.
They haven't put him back in sync.

He tries to focus on his movements, starts with his hands, his fingers. Flexing them gently and trying to keep the movement purely physical. He concentrates on his words, on moving his tongue and lips, exhaling and inhaling at the right times.
After two weeks he can speak without focusing again.

After a month he can walk without falling again, legs keeping pace.

Nightmares still startle him out of his body, jumpscares and loud noises do too, but he stops reaching for pencils with arms no one else can see.

Scratches sting again, headaches throb, and he doesn't even mind the pain, because with it comes softness and cold and warmth and texture.

And finally, finally they go back to Gravity Falls, and Mabel runs her hands over the trees and the planks of the shack and keeps hands on the formica of the tables at the diner, and Dipper welcomes the itch of heat on his skin, the grime of the dirt and leaves he gets covered in when he goes exploring. It is, however, an immeasurable advantage when the heat becomes stifling. Stan and Mabel both look ready to kill him when he comes back from a trip to the woods without his body. He just smiles at them, and Ford laughs in the background.