I think Sensei's past is the linchpin to unravelling the most mysteries. What was his relationship like with Amy's mother, and his brother? What happened with him and Maya and Noriko (what happened with Nikki seems fairly evident at this point)? I think the answer to these questions would help explain a lot. I also think what's in the boxes Maya has Sensei carry could clear up some stuff.
On the other hand, there are others I think it wouldn't help us answer. Such as 'what is buried beneath our feet?' or 'just how many "gods" are there screwing with us, and what do they want?'
There've been a lot of theories about all these things throughout the forum. Personally I think Amy's mother was significantly older than Sensei, and took advantage of him. I think he and Maya were definitely in a relationship prior to the cycles starting. I think there was a tragedy beyond the accident that took Amy's parents from her, which involved at least Maya and Sensei. Whether or not either or both died/came close to dying and are on some kind of life support I'm not sure. Whether or not pregnancy is involved somewhere - again, I'm not sure. I feel like there's potential for Sensei's relationship with Amy to not be Uncle/Niece, but I'm not sure.
As to the gods, I think there's at least 3 we've heard about - "Hope", the god of wires, and Yasu's eyeless god who at one time had plentiful eyes. Nozomu might be a 4th. I have no clue what any of them want. Nor do I have a guess, yet, what's under our feet. Also no guesses as to what's in the boxes.
In the end, it's hard to feel sure about anything, because the clues are obscure, and they come in bits and pieces, but there's enough to make you feel like it's slowly coming together. I also feel like there's connections I could be making and aren't - either because I don't know enough information about Japanese culture, or other similar knowledge gaps.
Anyway, that's my current take on things.
