Gravity Falls Plot

GF overarching plot: Stan and Ford are twins who decide to sail around together. They grow up and Ford wants to do other things. Stan accidentally breaks his machine and makes Ford angry. Stan is kicked out. Ford goes to university and becomes PhD. Stan becomes a conman and lives in poverty. Ford decides to move to Gravity Falls to study anomalies and call McGucket to help him build an interdimensional portal. The experiment fails, McGucket quits. Some time passes, Ford calls Stan. He asks him to hide Journal 1, because he already hid the other 2. Stan disagrees, they fight, and Ford is sucked to the portal. Stan tries to bring him back, fails, and decides to make a living off the Mystery Shack, with his brother's stuff. 30 years passes with Stan trying to bring Ford back and making money off the shack. Dipper and Mabel are sent by their parents to spend their summer in Gravity Falls with Stan. They both are forced to work at the shack, but one day Dipper stumbles upon Journal 3. After a few adventures, they meet Gideon, who used the powers of Journal 2 to gain the trust of the town. Gideon and Stan are great enemies because of the competition between the Tent and the Shack. Gideon wants to take over the Shack, Dipper and Mabel prevent him sev'ral timez. Dipper's mission of the summer is to find out who wrote the journals. Mabel's mission is to have an epic summer romance. Gideon makes a deal with Bill Cipher to steal the code to the deed of the shack. The twins stop Bill, Gideon breaks the deal and steals the shack by force. The twins and Stan stop Gideon and show to the town that Gideon is a fraud. Stan gets his hands on the other two journals and sets the portal in motion again. Dipper recovers the journal and finds the author's secret hideout, in which he finds a laptop. The twins try to discover the secrets of the laptop, but are stopped by Bill. Bill is once again defeated. The remains of the laptop lead them to McGucket. Together, they find the secret society that McGucket created because of the failed experiment with Ford. They find out that McGucket worked with the author in the past. Stan finally gets the portal to the point of bringing his brother back, but his shady past makes the twins stop trusting him. They nearly stop the portal from completing its activation, but Mabel decides to trust Stan. The portal opens, and Ford gets out of it. Stan reveals he stole Ford's identity to avoid issues with his criminal past. Ford desmantles the portal and finds an interdimensional rift. Gideon, on prison, decides to summon Bill again.

That's as far as we got from actual plot. Notice how the bunker itself wasn't important, nor the actions of the society, nor the agents.