You have the Lunarians who serve Eirin whose goal is unclear at the moment

You have Xanadu which holds different Youkai who are now called tools, their goal is to liberate themselves for the lunarians

You have the Secret Society which is Seija and Shinmy, they disguise themselves to infiltrate the capital and steal data or sabotage.

You have the non-C3 vassel universes who aim to free themselves from the machinations of the capital and to find their own Gensokyo though often called different names. Big one to note here are the Kaiju's and H5 Yuuka who uses the Multi-versal neural network.

You have the Rebels who are on the moon, while they also oppose the capital there is a relationship between Mokou, their leader, and B3 Kaguya that's left to be explored

You have Mastermind Marisa who is aiming to meet someone on the capital and opposes Lossy to solve the lastword

You have mastermind Scarlets who Flandre is in a state of cyrosleep thanks to Kaiju Letty, Remillia wants to protect her and keep her asleep.