Deep under Tokyo is the Underground. In this underground world, there are people who have special powers, some can control fire, water, ice, etc. Very rare are the ones who can control the power of gravity. Chelsea Rorec is a gravity user and is assigned by Company, the corporation overseeing the people of Underground, to protect the Maiden of Life, Ruri Sarasa. However, Ruri is really sad having to live in Underground and not seeing life in the real world. Chelsea, in granting Ruri's wish, takes her to above ground, and in the process, branded a traitor of Company.

When they get above ground, the realize that they are on the property of Asagi Rumina, a first year high school boy. They thus take shelter in hs house. But the assassins of the Company come after Chelsea and Ruri and after Chelsea is beaten by Seki's flame, Rumina tries to help. But Seki kills him in one move. After seeing an innocent person die for her sake, Ruri unleashes her power and brings Rumina back to life. Revived, Rumina beats Seki with the power of the wind, an elemental power that none of the people of Underground are able to control.

Tokyo Underground progresses on as the attempt to protect Ruri's happiness. More and more Company assassins come and Rumina and Chelsea are finally beaten by Pyron and Taylor Ashford. Both Chelsea and Rumina vow to get Ruri back from Underground.

This anime series is complete with 26 episodes.