Episode One of Blue Seed begins at a construction site, where Kaede Kunikida has disappeared underground.  Ryoko Takeuchi has gone in after her to try and bring her back, but Kaede is unwilling to return, intent on finding out the meaning of her destiny.  She disappears in a bright pillar of light and the story switches focus, to Izumo and Momiji, whom we first glimpse performing a ritual of purification. 
    Momiji finishes her ritual, but not before sensing that something is out of place and starts out on her way to school.  Before she can leave the woods, however, she is accosted by a young man wearing a red overcoat, with blue beads buried in his skin.  He starts telling her things about herself that she never knew and at first doesn't believe.  And then he tells her that he is going to kill her, but is unable to do so because of the appearance of a monster and then the TAC.
    Momiji is a bit overwhelmed by everything and is more than a little preoccupied when she arrives at school.  After a brief conversation with her friend Akiko, she goes to the library to research the things that the young man  told her about the Kushinada and she learns the story of the god Susano-oh and how he defeated Yamato no Orochi to save the Kushinada.  Momiji still doesn't understand what the legend has to do with her and while she is contemplating it, she hears Orochi call her name.
    Orochi then attacks Momiji while the TAC race towards the school, trying to save Momiji from the Aragami monster that towers above the school as they approach from the distance.
    This is the end of episode one and the beginning of Momiji's incredible journey.