12-year-old Misaki Suzuhara has just gotten involved in Angelic Layer, a battling game using electronic dolls called angels. Even as a newbie, Misaki shows advanced skills as she meets new friends and enters Angelic Layer tournaments to fight the greatest Angelic Layer champions of the nation.

When people dream, they express their utmost desires and emotions within the confines of their mind; but when their strong emotions cross the border into reality, the dream can turn into an uncontrollable nightmare. Touko and Rinko are sisters known as "yume tsukai" (dream users), and their job is to take care of these nightmares. Using toys as weapons, the girls must both destroy the nightmare and return the dream to its rightful owner before the nightmare does any sort of serious damage.

Upon reaching the train station to death, a dejected soul is informed that he is lucky and will have another chance at life. He is placed in the body of a 14-year-old boy named Kobayashi Makoto, who has just committed suicide. Watched over by a neutral spirit named Purapura, the soul must figure out what his greatest sin and mistake in his former life was, before his time limit in Makoto's body runs out. He also has a number of other lesser duties he must complete, such as understanding what led Makoto to commit suicide in the first place and learning how to enjoy his second chance at life.

Arale and company arrive at a nice location for a picnic. They soon discover a beautiful stone with strange powers. Before they know it, a dangerous pirate and his mysterious ship invades their peace and steals the stone. Now it is up to them to retrieve the stone before it is used by evil hands.