The very beginning of Episode 1 is the introduction of the series. It tells how Nurse Witch Komugi was born and introduction of each character and their relationships.

Angrar, the king of viruses, escaped to Earth from Vaccine World. The goddess of Vaccine World ordered Mugimaru to capture Angrar. Mugimaru asked Komugi to help him. This is how Magical Nurse Komugi was born.

Komugi and Koyori are good classmates. Kaneda-kun, their classmate, is infected with viruses and withdraws himself from outside world. Maid Koyori, who appears to be a rival to Komugi, brings out Mona, a character from 2-channel (which is a anonymous bulletin board web site in Japan). Mona infects everybody out there and turns them into all sorts of weird 2-channel characters. At last, Komugi and Mugimaru destroy Mona and capture the virus which infected Kaneda-kun.