When I first played Puzzle Agent, I didn't bother listening too hard to the clues, due to my believing everything would be answered in the game. When I was left with the slightly cliff-hanger ending, I just considered that perhaps there was no answer, and that the game wanted to keep things mysterious like a supernatural horror story. However, we know that a sequel of Puzzle Agent s coming out, and that it will have answers. Considering there's a whole story due to a sequel coming out (one of the designers said he had an entire story written, forget his name), I decided to play through Puzzle Agent again, but this time picking up all the clues. Now, let me give some thanks to YouTube commenter loo0oolNoo0oob for saying this in the Puzzle Agent 2 trailer "The moon resembles "The hidden people" face. Does that mean they have to do anything with the moon? Also remember after you fixed that puzzle guy brain at the hotel? He did mention 'Whispers from the moon' We're getting into something deeper now.." When I first read the comment, I blew it off quickly as poppycock. Then I started thinking a day or two later. The Gnome face on the moon and the guy mentioning the moon weren't the only hints. You dream of an encounter with an astronaut, and you also dream of being in a space station. Could perhaps this explain the gnomes and their goal? I immediately went to searching for clues that pointed to these Gnomes being aliens, and I found some VERY strong points. This is not just speculation mind you, this has some hard points. While I cannot explain everything with backup, I think it's pretty clear where these Gnomes are from and what they want. So, I will now give you my findings. I will first explain my findings on the gnomes, and then on what happened with Issac and Lobb.
Our first hint is on the newspaper Tethers has in his office. "Astronomers note new moon." Now the article title does not indicate whether this moon is over earth, or whether it's over some other planet. I would imagine the second choice, since a second moon over earth would be a very big thing. One you wouldn't just casually mention in an article deep in the newspaper. In any case, if this is the moon where the Gnomes are from or not, it still points in the general direction of moon and space.
The second hint is the mysterious astronaut that writes Scoggins on the crossword puzzle. While I do not know who the astronaut was, I do not think it was a gnome, since when Tethers sees a Gnome in Scoggins for the first time, he almost doesn't believe it. If he had seen one in his dream, you would think he would recall. In any case, this is yet another item that points towards the idea of the Gnomes coming from space.
Now this third clue is not as strong, but it's still worth mentioning. The Scoggins sign has a full moon on it. This doesn't prove much, but it's still a sign (no pun intended) of the moon being the Gnomes home.
Now we come to Bo. Now let me point something out. When Tethers sees the Gnome whispering into Bos ear Tethers screams when the Gnome looks at him, which seems to break the process of the Gnomes brainwashing session when Bo screams in response. Since Bos brain is messed up due to you breaking the brainwashing, his mind is filled with just puzzle fragments. Now, after you fix his head, he says a VERY telling clue. "Whispers of the moon CRASH too loudly. Clear the path." Let's analyze this statement carefully. Whispers of the moon, if the Gnomes are the people of the moon, then the whispers from the moon would be them. CRASH too loudly, the Gnomes must have crashed here on earth. "Clear the path," the Gnomes need the citizens to help them back to their home or take over the earth. Now we're getting somewhere.
The fifth clue is one that seems too convenient. The cult symbol for the Hidden People followers is shaped like a crescent moon.
The sixth clue is another biggie. When you are dreaming you are in that spaceship, you can see on one side that you re overlooking earth (the view of the moon?) and on the other side is where the Gnomes are at the moment, Scoggins. For some reason Issac is here as well, but he doesn't seem to have his full conciseness here since he never answers your questions and freaks out when the ship starts to malfunction. Now here's where things get interesting. Supposing the Gnomes crashed on earth, that must mean something went wrong in their ship. Could this dream be some sort of vision of the past of what happened in the Gnomes ship? I think it's quite possible. (A small explanation on Issac being there: Since the gnomes are already whispering to him as evidenced by his actions in the factory, perhaps part of his consciousness is in the same situation you are, but since he's fighting their whispers (or they are engulfing him in too many) he cannot think clearly)
Now this is more of a hunch due to my constant science fiction reading and watching. Bjorn said that Isaac was "lucky" to be chosen and that it is a great "honor." When Tethers asks him WHAT Issac was chosen for, Bjorn says "That is not for us to ask." How many science fiction stories are there where some aliens take advantage of the humans thinking they are gods, so they can use them for nefarious purposes? The last line I mentioned above that was said above seems like a common line said by many blind followers of fake gods.
The final clue is another small one. While you are approaching Issac in the factory, you here him mutter, "If the circumference of the earth is four times that of the moon." This may have nothing directly to do with the Gnomes, but it still points to the moon.
So, how does all of this fit together? Here's my theory. The Gnomes are from the moon (or a moon), meaning they are not of this world. While perhaps observing earth, something went wrong and they couldn't figure out what to do, so they crashed on earth, conveniently in a town where people worship gods who look like them. How do I know they crashed in Scoggins? The explosion in the factory couldn't be explained, perhaps the ship crashed in there? It's certainly plausible. In any case, after crashing, the Gnomes knew they needed a way to get back home. However, it appears they cannot do it themselves. The reason why they cannot get back home on their own would most likely be that they cannot solve problems on their own. For some reason, maybe they can think up puzzles, but they cannot answer them, which is why they have subjected some citizens of Scoggins to their whispers, to see who can answer their puzzles. Once they could find someone smart enough to figure the puzzles out, they would take that person to help them rebuild their ship. But why Issac Davner? Remember when Daryl mentioned Issac was from college with a degree? This is good evidence that he was perhaps a brighter bulb than everyone else. Being the smartest, the Gnomes decided to try and get Issac. Notice I say try, because their attempt failed due to friend power. This brings me to my second finding.
The picture in the lodge gives a very telling clue. We know that Issac and Lobb were both part of the cult, and that they were good friends by looking at how they lean on each other. Considering that the Gnomes were looking for the smartest person in town that could help them, and that this cult acknowledged them (in a sense), they probably tried the people in the cult first. While Bjorn and the rest, being more mystical, immediately took the gnomes to be the spirits and listened to everything they said without question, Issac and Lobb actually questioned what these Gnomes were and what they wanted. Realizing that being "chosen" by these Gnomes was not a good thing, Lobb and Issac may have very well had to run from the Gnomes and the other cultists which explains the torn orange fabric ob the lodges sign. But what about the lock, why is Issac locked up in the factory? I'm kind of surprised people think the Gnomes locked him up in there. When Lobb says his last words to you, he says "They tried to take him. They must not open the lock. Here's the key." I have paraphrased his words of course, since he said all this in a shivering tone. However, this is certainly what he said. Whether the cultists or the Gnomes themselves tried to take Issac, they obviously failed. If "they" must not open the lock, that must mean that they didn't put it there in the first place. But who did? Lobb. Lobb called the gear that he was holding the "key," meaning that he must have designed it to keep Issac safe. So why was Lobb frozen dead on a tree stump? Perhaps, once the gnomes saw that Lobb had saved Issac from them, they tortured him (as punishment) with thousands of puzzles until he froze to death. I say they tortured his mind because his hands are wrapped around his head, not his arms, meaning getting out of the cold was the least of his worries. Another hint that Issac put himself in the factory to protect himself is that, one, he kept begging you to stop getting closer to him, two, he would get upset when you got past his barriers, third, the Gnomes themselves helped you when the button fell out. Wanting to get Issac, they certainly wouldn't mind you making the way to him easier to get too. Issac's question of "why" shows he doesn't know why the Gnomes want him, but he knows it's not a good thing.
So, the Gnomes must have started subjugating some people of Scoggins to their whispers, in an attempt to find the smartest person. Some accepted it, even though they couldn't figure the puzzles out (the hippies), others succumbed to it, perhaps because they couldn't defend their brains against it, (Bo), and others heard the whispers, could figure them out, but realized the puzzles would only get more numerous should they continue to solve them. Wouldn't you start to go crazy if you were bombarded with hundreds of puzzles, and were expected to solve each one? In any case, it's obvious you cannot protect yourself form the whispers, as Issac himself was already being subjected to them in the factory. Somehow, it's possible to hear the puzzles without the Gnomes directly whispering into your ear, as evidenced by Bo. Whether the Gnomes want Issac to help them take over earth, or just get them back to the moon, I cannot fully answer, but it is clear that they are not exactly angels and that they are not from this world. While I have found some answers (or quite strong theories), I still look forward to Puzzle Agent 2 for confirmation and other answers (plus, I enjoy the puzzles).
Comments or additional theories? I might have missed a few things.