The children of Usui and Misaki met a boy in Kyoto and oversaw some strange miracles there.

It's the special One-Shot of Kaichou wa Maid-sama!

From Tokyopop:

Brilliant and overachieving, Misaki Ayuzawa is the President of the Student Council at Seika High School, formerly a boys' school. Unfortunately, most of the students are still male and stuck in their slovenly habits, so man-hating Misaki really socks it to 'em in an attempt to make the school presentable to attract more female students. But what will she do when the sexiest boy in school finds out that after school, Misaki works in a maid cafe.

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Also included in this manga is a short story called Toumei na Sekai in volume one.

Kouga Nagahisa never tries his hardest in life and he's in love with the prettiest girl Hananoi Mizuki. Mizuki has her childhood friend Kusakabe Riki who is the star of the basketball team. When Nagahisa gets home after school, he's in for a surprise.

The "military history story concerning boys and girls" revolves around Yuki, a girl who has lived in the rural area of Kyoto with her six childhood friends who all share a secret that they cannot tell anyone. On her 16th birthday, Yuki's fate begins to change.