The plot is that throughout Gensokyo, spellcards and such are used. Of course, this is the system that is used in all danmaku battles. Rogus, who fights using his heart and soul (Light and dark, Oblivion) came to Gensokyo because he felt that this way of fighting reduced youkai's, Humans, and Fairies thoughts.
He came to Gensokyo, and having his powers of Dimention crossing, he splits a hole in the Hakurei Border and this cut Spellcards power to the point where its just writting on paper. Rather now, the mind and soul are more open, and attacks and spells are more free and more controlled. Marisa, being the one with the powerful Master spark, didnt like this, because her spellcards were reduced, she followed a source of strange energy to see if she can get her spellcards working properly again.
Sakuya, noticed that because of this drop, Remillia has fallen ill. Remilia couldnt leave her bed, because her power was drained. Sakuya promised that she would help her get better, but she noticed that her abilities were dropping as well. On the same matter, she went out to find what was causing Remilias illness.