Yumiko Ichinose runs away from home to join the Anehara Cross School of Magic. On the way there she is accosted by a powerful mage who demands her grandfather's staff and is prepared to kill to get it. When she does finally arrive at the school she meets a strange girl called Koyomi Morishita, who insists that she knows her. However, their 'reunion' is cut short when they are once again attacked by Guibarthez.

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Koyomi Morishita decides to join the Anehara Cross School of Magic but soon finds out from Misa Anehara that the school no longer exists. However, later whilst visiting Akihabara she once again encounters Misa and gets caught up in the world of 'Modern Magic'. After assisting her in capturing two criminals Koyomi finally earns her chance to study under the famous Misa Anehara.

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Kaho and Koyomi are both now studying Modern Magic under Misa but Koyomi can still only produce pans. Later Koyomi meets Yumiko Christina Ichinose a powerful mage who is on the trail of a dangerous Daemon. The duo end up joining forces in order to catch the Daemon and retrieve Yumiko's stolen underwear. However, they soon end up involved in something far more dangerous.

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Yumiko goes to Misa for help in finding the mage responsible for summoning the Daemons, and soon Kaho and Koyomi have been recruited to help too. It isn't long before their 'investigation' leads them to the local water park, where Kaho tries to teach Koyomi to swim. However, after Koyomi nearly drowns it becomes clear that there is a Genie terrorising the park. As such Misa and the others must stop it before anyone is seriously hurt.

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Six years in the past, Koyomi tries to explain the reason she has come back in time to Misa and also to find away to get home. Meanwhile, Guibarthez is still pursuing Yumiko to gain possession of the Sorceress's Library.

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Still in the past Koyomi decides joins forces with Yumiko in order to stop Guibarthez rather than returning to her own time straight away. However, when Guibarthez manages to get a hold of Kerykeion the girls may no longer be able to stop him, and even the timely arrival of Misa may not help them.

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Upset at her inability to use magic Koyomi decides that what she needs is a magical item to improve her skills and as such she heads to Shibuya with Kaho and Yumiko. However, even with her new Tortoise rucksack she is still unable to use any magic except her summoning spell.

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Whilst investigating the connection between the various Daemon cases, Misa receives an email claiming that there is a bomb on board her flight home. However, when her search turns up nothing she realises tha the bomb threat has been nothing but a diversion. Meanwhile, Koyomi and the others decide to surprise Misa whilst she is away by cleaning up the house.

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