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Chizuru Yukimura has come to Kyoto looking for her father, a doctor who has gone missing. While there, she witnesses a fight between an Oni and the Shinsengumi. Taking her into custody, the Shinsengumi debates on what to do with Chizuru, when they discover that she is the daughter of the doctor for whom they are also looking. The Shinsengumi then take Chizuru along on their search after the missing doctor, from adventure to adventure.

The school love story is set at Baramon High School, a private boys' school for the prefecture's most elite. The protagonist is a seventeen year old boy who transfers into the school and meets various major players on campus, such as the outlaw teacher, the soccer captain, and a childhood friend whom the protagonist has not seen for seven years. The school presents opportunities for friendship, love and conflict, and changes are now bound to happen in the main character's life.

The series began in the middle of a game of hide and seek, as a young boy named Justin Casey (Gen) finishes counting and begins searching for his friends Angela (usually called "Angie") and Corkey Roberts (Kanna and Tsukubo Natsuyama). As he searched for the brother and sister in the wooded area, a storm occurred all of a sudden. Justin managed to sneak up on the two before the rain started pouring, forcing them to run for cover. They would eventually find a house in the wooded area, previously unseen according to Justin. At first glance it appeared nobody was home after entering the house, until they discovered a robot named Solar Ion Robot (Kadenchin), or the acronym SIR. They would soon meet the owner of the house, Professor Humphrey Bumble (Dr. Tokio Taimu), who introduced the children to his greatest creation, a time machine. Professor Bumble's attempt at recreating Benjamin Franklin's famous lightning experiment with the use of a kite flying outside the house to get the machine working only led up to SIR's temporary change in personality before sending the entire house on course for the past. The children never realized how long the journey back home would be due to Professor Bumble's misguidance and errors in time travel, but in the meantime they witnessed and participated (with little or no consequences) in numerous events in the Bible's New Testament, from John the Baptist's birth to the rise of the Apostle Paul."

 Maiku Kamishiro’s past has always been somewhat of a mystery to him. The only clue he has to who is family might be is an old photograph showing two young children, a boy and a girl, playing in a small pool outside of a blue house. In an attempt to find his family, he moves to this blue house and begins working as a programmer. He’s living a comfortable life until the day two very different girls show up at his door, both in possession of the same photograph, and both claiming to be his twin. With no way to prove who is a relative and who is a stranger, Maiku allows both girls to move in with him until they know for sure.