2095年，魔法不再是一种虚无缥缈的幻想，而是一种已经应用了近一个世纪的科学技术。 在例行的新生入学的春天，国立魔法大学附属第一高中，通称“魔法科高中”，迎来了一对兄妹。 哥哥是什么事都拿得起放得下的“二科生”，而妹妹是对兄长抱有超越血亲感情的完美无缺的“一科生”。 伴随着两人的入学，平稳的日常生活开始变得波澜万丈。

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