Disclaimer: This is just a fan speculation of Touhou Project - Hidden Star in Four Seasons and does not reflect what may actually be happening in Gensokyo.
So far, I've been wrapping around my head on just what kind of mythology can possibly relate to the four seasons. After some googling (as usual), I think I'm beginning to piece together some ideas that can clue in to the culprit.
First piece of puzzle is the title itself: "Hidden Star in Four Seasons". Based upon using the term "star", we have an implication of constellation. Some people postulated that this could be referring to Southern Cross (
https://en.wikipedia.org/wiki/Crux), which is not visible to most Japanese region.
Then we have the four seasons. We have had incidents playing around with manipulations of season before (TH6, TH10.5), but it seems like the seasons are happening with geographical relevance this time.
Spring - Hakurei Shrine - East - Azure Dragon (蒼龍)
Summer - Foot of the Mountain - West - White Tiger (白虎)
Fall - Youkai Mountain - South - Vermillion Bird (朱雀)
Winter - Forest of Magic - North- Black Turtle (玄武)
Fanmade Map of Gensokyo may help visualize:
http://orig08.deviantart.net/00d4/f/2010/128/a/e/gensokyo_traditional_map_by_captainonimaru.jpgAs hinted above, the four seasons are "personified" as gods in Chinese mythology called "Four Symbols" (四象). These four entities have appeared frequently in Japanese media (ex. Digimon) as god-like entities overseering their respective regions. They are also representation of seasons, among tons of other things they are associated with (elements, animals, force of life, etc.).
The Four Symbols also have very close ties to Chinese Constellation called "Twenty Eight Mansions" (二十八宿) (
https://en.wikipedia.org/wiki/Twenty-Eight_Mansions). The idea is that these Four Symbols are summation of 7 sub-constellations in East, West, North and South. Each of the sub-constellation have a certain meaning, and they act like "body parts" to the Four Symbols.
What may rule them over are the constellation in the middle (中), and this is known as Three Enclosures (三垣). This is known to be where Jade Emperor (
https://en.wikipedia.org/wiki/Jade_Emperor) is housed, along with his government officials, etc. It's also popularized in the media as the being that is above "the Elite Four" (
http://tvtropes.org/pmwiki/pmwiki.php/Main/EliteFour) (
http://tvtropes.org/pmwiki/pmwiki.php)./Main/TheFourGods). Personification of such being standing in the middle is usually referred to as Kirin (麒麟) (
https://en.wikipedia.org/wiki/Qilin).
While Kirin is recognized as the Central Leader of the Four, we are not clear as to which "star" of Chinese Constellation it represents.
It very may well be that the future direction of TH16 to locate the "Center" after figuring out the geographical location of Four Seasons are happening, and find out that culprit is able to master and control some kind of energy that allows willful control of the seasons.
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Just for Laugh PS section
PS1 Kirin is so gentle that she'll get beaten up even by Cirno and be okay with it
PS2 The culprit is Satsuki Rin, ZUN is bringing her back from the dead pixels of TH6 (or reincarnation of it)