The energetic Mikan and calm and collective Hotaru have always been close friends despite their opposite personalities. Hotaru has always been a genius creating amazing inventions while Mikan has always been interested in her friends. One day Hotaru's abilities are noticed by Alice Academy in Tokyo.

After Hotaru leaves for Gakuen Alice, Alice Academy, Mikan is devastated and runs away seeking out to be reunited with her best friend. She learns that students of Gakun Alice have special abilities known as “Alice” and that after being stopped by security that she also has these abilities and is enrolled in the Academy. Despite finally being able to meet Hotaru again, Mikan learns things aren’t as easy as they always seem.