Shuffle is about an average 17 year old boy, until 2 new girls are introduced to their school, announcing that one is the princess of the gods, Lisianthus, and the of the demons, Nerine. They both wish to marry Rin, making him king of either world.

Whilst being in the situation, his childhood friend Kaede, an old friend Asa and a younger friend of Narine, Primula discover themselves to love Rin also.

Rin must decide between 1 of the 5 girls, breaking 4 of their hearts.