Japan, present day: Alien Invaders are everywhere, taking over peoples' bodies. Fighting them is Isuzu Ayane, an introverted young girl with the ability to control powerful dimensional Gates. Under the guidance of Kageyama Reiji, a mysterious businessman, she battles Invaders and recruits new Gate Keepers. Will she and her new comrades be able to save the earth?
Some years into the future, a strange, unexplainable natural disaster has broken off a piece of the Japanese mainland. Known as the Lost Ground, it is now inhabited by people with Alters -- machine-like extensions of their own will. In order to keep the peace on the Lost Ground, the HOLY organization uses its own Alter capabilists to police the region. In the midst of the chaos is a young man named Kazuma, whose life will soon change forever as he discovers his hidden abilities, and how to wield them.
Kamina Ayato may seem like an average boy in a devastated world, but after being captured by TERRA, a military organization set on saving the world from the Mu, an alien race set on "tuning" the world, he realizes he is an instrument in deciding the fate of humanity and piloting RahXephon. Not only is Ayato the only person who can control the mecha, but he also has a terrible fate of his own. Holding onto memories of his old life and grasping to keep his own humanity, he must struggle in this new world and realize his true potential with RahXephon.
Kamui has returned to Tokyo with a traumatizing past, but he is not the only one. Many people are returning to Tokyo for the same reason: they play a part in the End of the World. The Dragons of Earth and the Dragons of Heaven now must fight for the destruction or safety of the world. But is this troubled Kamui really the key to saving the world?
While transporting bio-weapon lifeforms, Agent DD, member of an alien police force, is forced to crash land on Earth. Amidst the chaos of the crash, a bio-weapon escapes and DD is forced to fight it, while accidentally activating a Liberus, a liquid battle suit. Tsubasa, a shy girl, unwillingly comes into contact with the Liberius and is thereafter forced to fight for the survival of Earth.
Under Tokyo there is a city where select people have a natural ability to control the elements. But when an uprising takes place, Chelsea Rorec helps Ruri, a mysterious girl known as the maiden of life, escape from this secret world. Together, they stumble upon Asagi Rumina, a man who becomes determined to protect Ruri from those who pursue her; though unaware of the power he's up against, the task will prove difficult to say the least. Now, with his newfound powers to control the wind, Rumina must save Ruri, theu nderground and the surface world from ultimate doom.