My vote is that Keine manipulated the course of history so that Yukari would manipulate Koishi into becoming bored enough to subconsciously manipulate Parsee to cause jealousy on Nue, who uses her pretext of being jealous of youkai siding with humans to hide her true motivations.. which is.. she's really jealous of youkai siding with humans.
Meanwhile, Cirno was watching Keine's movements with caution, and sent her friend Daiyousei to investigate the outside world, since there were enough clues that the humans from the outside world have actually received technology, speeding up their development and thus, forcing Kanako to move to Gensokyo earlier. Who could benefit from this? The Kappa? The Tengu? Shinki? The lunarians? Eirin?
On an early morning, Akyu received an uncommon visitor at her home. Komachi has reported on the various activities during the previous incidents, and brought confidential information from the Scarlet Devil Mansion and the domains of hell. Akyu has then become able to confirm that Remilia's purpose for staying in Gensokyo was to measure the military powers of its inhabitants, under the orders of the lunarians. Komachi also reported that Sakuya was murdered, around one year ago, and replaced by an imposter, because there were other people that were suspicious of Remilia, and wanted to keep an eye on her. But, who could've murdered Sakuya, and/or have replaced her? Yumeko? Sanae? Yumemi? Patchouli?
There were many possibilities; The three fairies were mysteriously absent from every major incident, or so, they are thought to be. Orange, a long-time enemy of Rumia, who was known as the Dragonslayer back then, hasn't been seen since LLS as well. The two humans from the Outside World may have been given the means to persuade Yumemi to travel in time and inform the humans from some 1000 years ago about Byakuren saving the youkai, which resulted in her sealing. Kourin may have been responsible for the database disorder that resulted in Reimu and company having harassed Makai in MS, but why? The fact that Vivit was able to meet Marisa and Reimu and defeat them could mean that Luize not only had the means to bring her where she wanted her to be and when, but had a hand in the events of Shuusou Gyoku as well, and even in the creation of Vivit herself?