It's not like the Gravity Falls universe was the first one Bill Cipher had taken over. The previous one had been when he'd made a deal with a high school girl named Junko Enoshima, infecting her with an unstable...unfathomable amount of despair. It spread like a disease, first infecting her classmates-ultimate high school level classmates-who carried it across the globe. Bill had done his job, so he left the rest to Junko, the self-proclaimed "ultimate despair." Though he would have loved to watch her put on the first mutual killing game in the school itself, he had other business to attend to. And that business was in a sleepy town in Oregon, U.S.A.
What attracted him here was good enough to pry him away from his success in the last dimension. Oh, how he loved seeing entire populations destroy each other. But he couldn't pass up on an opportunity like the paranormal magnet known as Gravity Falls. Not too long after his arrival did he find a perfect host for despair. One who Bill had given the alias of "Pine Tree." Dipper Pines, a boy who had come with his twin sister, Mabel, to spend the summer in Gravity falls with their great uncle.
Normally not too impressive a person, Dipper was the first to find the hidden Journal #3, making him an important piece of the puzzle that was Bill's plan. When the time was right, he would take over Dipper's mind and fill him with despair, just as he had done to Junko.
It was time to put his plan into action. When he wasn't scoping out Gravity Falls, he was monitoring his other chaos-filled dimension. Upon his latest visit, six had survived Junko's "killing school life" game and had joined the Future Foundation, a group whose purpose was to end all despair. Bill would hardly give any attention to such a pathetic cause. If it started to get in his way, he would have to annihilate it. But that didn't matter at the moment.
Though Bill was shocked to hear of Junko's defeat, it was not unexpected. She had to sacrifice herself for the cause of despair. Her mascot, Monokuma, was still the face of this world-ending event known as the "the terrible, most awful, most tragic event in human history."
What did matter was that one of the survivors, Makoto Naegi, dubbed "the ultimate lucky student" turned "ultimate hope", was conducting an experiment of his own. Class 77-B, the first group of students infected with despair by Junko, or the "ultimate despairs", were Junko's most loyal followers. By submerging his upperclassmen in a Psychotherapeutic Communication Simulator otherwise known as the "Neo World Program", he would rid them of despair by taking them into a virtual island where their memories would be replaced and trauma undone.
All Bill had to do was watch it unfold before him from the sidelines. Though he made frequent trips to the Gravity Falls universe to check on his progress, he couldn't miss how this all played out. He was a mind demon, after all, so all he had to do to enter the ultimate despairs' virtual world was slip into the mind of one of their suspended bodies which would connect him to the program. At first sickened by the general easygoingness of the island environment in which the subjects were all inhabiting, and the fact that they were avatars of their previous, despair-less selves, Bill was soon pleased to find that Junko Enoshima was, even after her death, not a force to be reckoned with. Her virtual AI was in the program as a virus, and would send the participants into another mutual killing game. He wanted to stay for the fun, but Bill had a new plan. This was the perfect opportunity to speed up the destruction of Gravity Falls. If Bill could get Dipper and Mabel into this killing game, it would fill them to the brink with beautiful, delicious despair.
That's how it all began.