Levi, a young girl with special powers, faints while running away after damaging her village from being unable to control her bursting powers. When she wakes up, she finds herself on the deck of a large ship with both her arms turned black. She had lost her powers from the uncontrollable outbreak back in the village.

The ship happens to be the home of a group of diverse sailors led by Captain, who suggests that they take Levi under their roof. Levi is disheartened when she realizes that she does not know how to do anything apart from using her powers. However, she soon learns to do many things herself with the help of the sailors. One day, as Levi gradually gains back her powers, Captain suddenly disappears. Levi and the sailors set off on a journey to find their missing Captain as they recall the clues he had left behind.