Sorry, I just returned after making and eating dinner. Right...recap. I'll do it from the Touhou POV.
Enemies appear. The Scarlet Devil Mansion is attacked, Meiling defeated (not killed), Remilia, Sakuya and Flandre go out to meet the enemy. The mansion is taken and is now under control by Orks, though Patchy has barricaded herself in the Library.
Imperials settle down in the Forest of Magic, setting up a temporary base.
Meanwhile, Necrons attack the Human Village. Reimu gets Yukari to create a shelter for the Humans, and Keine, Reimu and the UFO-crew evacuate all the humans (and Cirno).
In the Bamboo Forest, the Lunarians rise to defend the Forest from the Imperials and, later, Tyranids. Eirin and Reisen hack into the Synapse (the Tyranids' Hive Mind
) and manage to cause some chaos until Reisen can't take it anymore. Kaguya unleashes the Imperishable Night as a last resort, but in the end the Lunarians flee the forest, and Tewi escapes with the Rabbits.
However, an assassin is sent to kill Kaguya, and Eirin does a You Shall Not Pass
to allow Reisen and Kaguya to escape. Shredded to pieces, Eirin is saved by an Imperial Chapter Master and enters negotiations with the Empire together with Byakuren. They agree to aiding the Empire in the fight against the Tyranids and Necrons, in exchange for the Empire taking care of the evacuated humans. A message is sent out to prominent Gensokyoians to inform about the truce.
Eirin is taken aboard an Empire-ship to have her body fixed again, but is tricked and has her soul trapped inside a Rubric Marine by Tzeenecth-followers. She is saved and returns to Gensokyo to find Kaguya, last seen heading towards the Hakurei Shrine.
Meanwhile, at the Hakugyokurou, Yuyuko gets Imperial visitors who warn her of servants of Chaos drawing near. Sure enough, short time afterwards they appear and apparently does short work of Youki.
The Moon is under siege by Tyranids, fighting a fierce but hopeless battle against the invaders.
In Hell, a Mechanicus-expedition are enjoying the hospitality of the Oni, while the Hellraven and Kasha are on the surface burning Necrons.
...uhm, that pretty much covers the important bits. Please ask if there's anything you're wondering about.