Chiyari has discovered a grand piece of the conspiracy. A room with four capsules; two are open and empty but two more each have a Yuuka in them! In the terminal lies an ability card. Four of a Kind. That must be why the crystal wasn't able to restore Yuuka. She wasn't split into two; she was split into four! The Lunarians must have cut a deal with the tengu to get their hands on this.
But why the heavy machinery? If they wanted to multiply Yuuka, they would just need the card. The machinery seems to have some ability to alter behavior. Is this an attempt to place sleeper agents into Gensokyo?
Well whatever the truth is, everything necessary to restore Yuuka is here.

Ok, that's all I wanted to hold for.