This is more of a headcannon than an actual theory per-se, but I think Bill may be the one writing the ciphers at the end of each episode. He seems like enough of a trickster to do so, honestly.

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This is more of a headcannon than an actual theory per-se, but I think Bill may be the one writing the ciphers at the end of each episode. He seems like enough of a trickster to do so, honestly.
Finger Theory
I have a theory that I think fits pretty well in the Gravity Falls' universe and it deals with the Six Fingers on the books as well as the different fingers on the characters. I'll start with how polydactyly is often represented. According to Hindu mythology, additional limbs are a sign of strength, such as the deities known as the Asura, who seek constant power. Also in Hungarian mythology, the "Taltos" are shaman like people born differently than others, like being born with teeth or have six fingers. From childhood they are kept hidden in secret and act as healers and connection between God and the tribe. Probably one of the most well known multi-limbed entities can be found in the Bible from those such as the giants, more commonly known as the descendents of the Nephilim (often associated with the Annunaki)
2 Samuel 21:20,"And there was again war at Gath, where there was a man of great stature, who had six fingers on each hand, and six toes on each foot, twenty-four in number, and he also was descended from the giants"
The Nephilim are said to be fallen angels who formed relationship with humans and produced, "men of renown" a.k.a the giants from their union. In short, supernumerary are present in those in certain positions of power, and the more they have, the closer they are to the supernatural and/or control of it, bearing powers that are above natural ability (either physically or intellectually)
Looking at the people of Gravity Falls, we can see those who do possess more than just the traditional four (as is cartoon tradition), are more than meets the eye. Lets start with season 1 antagonist, Little Gideon. Loved (emphasis on the E D) by the town for giving them a taste of the supernatural through his fake seeing of the future. He has a charismatic power over people and know of the strange goings on of the town, seeking the journals for himself. Those who know Gideon most, more specifically his parents, know of his fake psychic game and still show a fear and submissive attitude towards him. When Stan turns on the portal, Gideon somehow senses it's activation, awakening him from his slumber in prison. He has five fingers on each hand.
Soos is another person with five fingers on the show, but hes just a loveable goofball right? Nothing otherwordly about him...or is there? While mostly just performing maintenance of the Mystery Shack, it has been hinted that there is something about him more than human. Even though it could be played for comedy, as noted by multiple people, during the episode, "Time Traveler's Pig" Soos uncannily reveals future events to Grunkle Stan. When fighting Bill Cipher in Stan's mind, Soos' attack (to me atleast) seems to hurt Bills most (aside from his own attack bounced back at him). If one's mental capabilities make them stronger in the dream realm, Soos seems to be stronger than Mabel and Dipper. Bill also points out that they are more clever than they look, especially the "fat one". When bitten in, "Scary-oke" by a zombie, while still craving brains, he is able to retain his personality while the rest of the undead are mindless monsters. A secret code revealed in the Gravity Falls game, "Rumble's Revenge" states that,"The handyman knows more than you think." The most unsuspecting (and only handyman) shown in Gravity Falls is Soos.
Others include Deputy Durland, Sheriff Blubs, Stan, and Old Man McGucket have five fingers and something to hide. Both policemen were entrusted with the secret of the founding of Gravity Falls that presumably only a few knew about (including the existence of the 8th and a half president), suggesting that the two have a higher position of power than simply town policemen, especially considering the fact that the location of the secret held a ton of more mysteries than just Quentin Trembley (such as a giant evil baby trapped in ice, santa claus being the real president, the real identity of Thomas Jefferson, etc). Stan Pines, as confirmed in the second season, knows of the supernatural entities of the town and seems to know about the power of the journals. His secret underground lab (possibly a testament to his intellectual prowess) has a portal that is able to go to different dimensions, though Stan seems to be looking for a specific one. Lastly we have McGucket, most might know of the leaked image which proves he is the author (or one of the authors) of the books. In this image we see him writing in the book with six fingers and no cast. Like some fans I speculate that it was later cut off by him or some sort of accident, which is why he wears the cast to begin with. In my opinion he is one of the most mysterious characters in the show. Constant hints indicate that he was in a constant struggle with something or someone (maybe multiple people) and eventually lost his mind. His youthful agility, high intelligence (shown in his multiple inventions), and construction of book 3 is evidence that he is probably the most connected to the supernatural and probably still is.
The power and control aspect of the six fingers fits in perfectly with Bill Cipher's goal. Each book could be a way to control the supernatural creatures as it not only contains the habits of the monsters, but weaknesses as well. They also look like a key to multiple dimensions (possibly the origin of all that go bump in the night) shown when Stan activates the machine he has to put the books on a certain platform. This theme fits along with the frequent Illuminati references. One could say, "The fingers are simply an artistic choice" but when asked about the fingers, Alex Hirsch responded in the same way he did to a question he deemed would be a, "spoiler question", distracting the audience with an hypnotic wheel to humorously avoid the question rather than give a straight answer.
You know how there are a lot of Eye of Providence's (or Bill Cipher's) all over the place? Well I think that how Bill "sees lots of things!" I think he can swap consciousness between each one to spy on everyone and everything. In addition, maybe that's how Gideon got the idea to use hidden cameras to "know" everything about everyone.
Bill... Bill Everywhere. Also, sorry that this layout is pretty bad. I couldn't find a way to get the whole thing to go vertically. And sadly, I can't split it into multiple images... Only one at a time >_<
13,44-
While I was watching "Dreamscapers", my sister (who doesn't like GF) kept hearing them say, "13,44-" and she noticed they never said the rest of it. So, like any person would do, she googled it. What came up was very interesting. If you find 13:44 in Matthew (the Bible) it says, "The kingdom of heaven is like treasure that was hidden in a field. When a man found it, he hid it again. He was very happy. So he went and sold everything he had. And bought that field." I thought this was very interesting to that episode. So what if there is a treasure hidden inside the Mystery Shack? I have no concrete evidence, but I thought there was no way this was a accident. Well, it could have been an accident because accidents happen all the time but its really unlikely and I'm rambling right now with stuff that doesn't even have anything to do with anything so I'll stop. Anywho, I thought this was too cool not to share so there it was.
Search for the Blindeye
Ok. The most recent code (from Gideon Rises) was "Search for the blindeye." This struck me as odd, and it got me thinking about how a lot of things in the show seem to revolve around one eye.
Stan sometimes wears an eye patch
Lazy Susan has a lazy eye
Bill has one eye
Birch trees have the pattern of a single eye on them (as seen in Dreamscaperers)
Each journal has a monocle- like glasses but for one eye
We've all seen how Old Man McGucket's eyes seem to wander, but what if one of them is actually looking in the right direction while the other isn't real? That means he would have one eye
Does anyone have anything else to add? Maybe covering one eye is symbolic and has to do with the secret society. This is just something weird I noticed.
WIP
Inking/Correcting/Colouring this: http://thelordofdoomydoom.deviantart.com/art/WELCOME-TO-GRAVITY-FALLS-KIDS-388025735 , made by the awesome "thelordofdoomydoom" of deviantART!