Haru Irei, who witnessed the 1/1 scale RX-78-2 Gundam in Odaiba, becomes inspired to build Gunpla, which is a portmanteau of Gundam Plastic model kit. Haru purchases a one of a kind gunpla, the GPB-X80 Beginning Gundam. After building the kit, Haru, now a Gunpla Builder, and the Beginning Gundam enter the virtual world of Gunpla Battle, where players can pilot their customized Gunpla in team matches or one-on-one fights. Haru must rely on the support of his friends if he is to become a Gunpla Battle Champion and attain the rank of Gunpla Meister.

Iwaki Tomonori is an average 15-year-old boy who likes older women. He happens to have a crush on his teacher, but soon thereafter, learns she has become engaged. He heads home brokenhearted, only to find a 12-year-old girl named Rizel at his home, who he learns the Japanese government has married him to against his will. Furthermore, he learns Rizel is no ordinary girl; she is a biochemically engineered human, and her creators (her "papa"s, as they are often referred to) promise to waive multiple bills of Iwaki's parents in exchange to be allowed to stay at their house, and thus Iwaki's life with Rizel begins.

After destroying the Zorbados Empire, the Jyusenki-tai/Cyber Beast Force has expanded and are training new recruits. But after failing to stop a monster that seems to be a remnant of the Zorbados Empire from destroying a city, the CBF is thrown in jail. Now the CBF have to escape from jail and find out what was behind the monster they fought.

Extra episode of Mahouka Koukou no Rettousei: Yoku Wakaru Mahouka! included in the BD/DVD.