The basic plot is as follows, Gensokyo has been ruined by Second Impact; a cataclysm caused by a contact experiment between Kanako Yasaka and the Master Spark that, among other things has killed off the vast majority of Gensokyo's male population. The organization Bishoujo Installation for Research and Defense, or BIRD as it is better known serves as the NERV of this universe; developing the weapons that our heros use. As Shinji Ikari is Alice Maragtroid- or as she is known in this universe- Alice Morichika. That's right: Alice is the daughter of Rinnosuke and Tenshi Hiranai- also known as Tenshi Morichika. It only gets odder from there.
Most characters in Neon Genesis Evangelion have some representation in a Touhou character; though several Touhou characters with no equivalent in Neon Genesis Evangelion also exist. Still in progress; being written by Katsuun. Can be found here: . Expect some Character Derailment, given that this is Touhou that we're putting into Neon Genesis Evangelion.