Ayato Kamina was separated from the girl he loved, Haruka Mishima, when an event occurred that was thought to have killed everyone outside of Tokyo. But one day three years later, invaders suddenly attacked the city. It was then that he meets an agent of TERRA, Haruka Shitow, who tells him that she will give him the truth about the world. It is the beginning of a series of strange events, which involve him activating a giant mecha, the RahXephon and finding out that many people, including his own mother, has blue blood, and that he was actually living in a self-encased dimension where time moves slower than that of the outside world.

Kokone Morikawa has a strange napping disease that distracts her from reality, one that makes the world of her dreams and the real world near indistinguishable. In reality, she is an average high school student preparing for her university entrance exams; but in her dreams she is a magical princess of Heartland, a machine-driven future where the use of artificial intelligence is forbidden. Within the seemingly imaginary dreamland, Kokone discovers more about her family's past and the secret that her father, a talented mechanic, has tried to protect her from. However, as the events between two worlds intertwine, she must now protect the secret from villainous entities, both dream-like and terrifyingly real.

Kotetsushin Jeeg takes place fifty years after the original and features a new cast of characters—primarily the new main character Kenji Kusanagi, a high school student who becomes Kotetsushin Jeeg to fight the sudden reappearance of "Haniwa Genjin" ("Haniwa Phantom Gods", or clay robots) from the Jamada Empire ruled by Queen Himika. Other characters include Tsubaki Tamashiro (grandaughter of Miwa Uzuki); and Kyou Misumi. Other main characters from the original series also appear.

A contest is made by the Fifth Hokage called Jonin vs Genin. The point is to collect crystals for points, with the higher-ranked Chunin and Jonin holding crystals worth more points. The Genin have blue crystals, while the Chunin and Jonin have red crystals. The video shows various fights between the Genin and Jonin, which each instance ending in the Jonin unknowingly losing their crystal (or discarding it). (Source: Wikipedia)