In a World Where Magic is Like Computer Code… Koyomi Still Hasn’t Learned Basic. Life hasn’t been fair to Koyomi Morishita. Even though she’s in high school, she’s so short that everyone assumes she’s still in grade school. The boys and girls in her school tease her mercilessly, and she’s not exactly graceful either. On the other hand, she’s still better off than Yumiko, who has a magician trying to kill her. Or at least Koyomi WAS until their paths crossed! Fortunately, salvation arrives in the form of master mage and graduate student Misa Anehara, who agrees to take Koyomi under her wing in learning the new style of magic, which breaks enchantment down into sequences of code. That’ll be quite a task, given that so far Koyomi’s talent seems to consist of making washbasins randomly fall out of the sky. But if it was easy, it wouldn’t be magic, would it? Get ready for a whole new kind of ‘spell’ing lesson as Koyomi takes a desperately needed crash course in charm school in Modern Magic Made Simple!
Misa and Kaho look on as Yumiko attempts to teach Classical Magic to Koyomi. Yumiko becomes highly frustrated when the only things Koyomi can produce are washbasins.
The young Yumiko runs away from her lavish lifestyle. By reading her grandfather's journal, she discovers that she can learn magic at the Anehara School of Magic. On the way, she meets Jean-Jacques Guibarthez--a man who wants her staff and will kill her to get it.
The storyline goes back in time when Koyomi arrives at the Anehara School and meets Misa, who, after a series of unusual events, agrees to teach her Modern Magic.
Daemons have been released, and Yumiko asks Koyomi to help her vanquish them, unaware that the only magic Koyomi can perform is summoning washbasins.
A trip to the water park turns chaotic. Misa seeks to find the source of the virus that brought the Daemons. The ladies prevent a possible disaster.
The past and present stories are told together. In the present, Koyomi travels back in time. In the past, the reason for Guibarthez's pursuit of the Kerykeion is revealed. Misa resolves to fight Guibarthez.
Yumiko and Guibarthez finally meet for battle. Yumiko and Misa show up to help. Recalling past advice from her parents gives Yumiko the tools to defeat Guibarthez.
Koyomi searches for an item through which she will be able to channel her magic. However, she finds that the only tool she needs is to believe in herself.
Misa reveals how her mother passed away and why she blames herself. Later, something goes wrong on her flight, and she saves the day just in time to get home for dinner.
Yumiko awakes with a sense of dread. Misa walks into a trap, and brings Koyomi with her. Once again, someone wants to obtain the Scorceress' Library.
The group goes to Akihabara in search of Misa. When they arrive, they encounter Huang and Guibarthez.
In Akihabara, Misa's ghostscript makes an appearance, but she is no help with locating her body. Soshiro is immune to magic, which comes in handy once Huang and Guibarthez show up.
The sorceress is now free, and she is using Yumiko's body to revive herself. Misa prepares a code to banish her to another world. The power of friendship proves capable of saving the world.