Long, long ago, there existed a world of magic and science. God, afraid of man's potential, split the world in to the world of science, Elde, and the world of magic, Fandavale. One day in Fandavale, a terrible witch named Cendrillon (Cinderella) revives. Cendrillon plots to rule both worlds, and searches for the "key" which holds tremendous power. A young boy from Elde by the name of Sōta meets a mysterious girl from Fandavale, Akazukin, and her talking wolf companion, Val. Sōta learns that he is the key Cendrillon is searching for. Now it is up to Akazukin, Val, and the other Fairy Musketeers to protect Sōta from Cendrillon and her Nightmarelians who wish to obtain the power he mysteriously possesses.

The final DVD volume contains two specials: Tokimeki no Yuuki Episode 18 (sometimes labeled 17.5), which was never broadcast on TV. It features the swim captain, Utsumi Koayu. Tokimeki no Sentaku Episode 25.5, a recap of all episodes but the last, which was initially displayed at the Konami booth for the Tokyo International Anime Fair in 2007.

Following the destruction of the magical floating device from OVA 1, the Magic Academy falls to earth, but unfortunately lands on and breaks a demon seal, releasing hundreds of ancient demons into the forest around the academy. The teachers are barely keeping the demons away and are desperately searching for the pieces of the floating device, so to earn more magic stones, all of the students from Amelia's class decide to leave the academy (even though they were told not to) to find the missing pieces. (Source: ANN)

The story begins when the kingdom of Noigllado suddenly invades the small country of Azuelgatt and brings it to the brink of destruction. General Adnowell leads Noigllado's troops against Azuelgatt's final, remaining line of defense: the fortress Doroah, led by a skilled female warrior named Shamshir. (Source: ANN)