Fuuma is a normal boy, and lives a normal life with his sickly younger sister, and Shinto priest father. His mother had died a long time ago, but they don't dwell on that. For them, keeping her memory alive by doing good is enough.
But who ever said CLAMP series are ever simple?
Fuuma's father dies, killed by an unknown person (who is actually a Dragon of Earth, and the sword passes on to Fuuma later in the series), and the holy sword, the Shinken that has been in their temple for six years is gone as well. Dying in Fuuma's arms, he tries to tell Fuuma of his impending fate, but fails and dies, leaving his son confused, and his daughter more traumatized than ever before.
They then come across Kamui's aunt, later kidnapped, then escapes back to them, only to "birth" another Shinken by allowing her body to be ripped apart as the sword comes out of her. The three teens are picked up by the three heads of CLAMP Academy, a school rooted in mysteries, and connected, once again, to the end of the world. They claim they can hide the Shinken they hold until the "promised day" comes, their school made solely for that matter apparently. The kids have hardly any choice in the matter, so they agree, and hear the whole story.
It's 1999, and the world is dying slowly. Fourteen chosen people from across Japan know this (aside from a few independent individuals), and gather in Tokyo, forming two groups of seven, the Ten no Ryuu or Dragons of Heaven or Seven Seals who dedicate themselves to protecting the world from destruction, and the Chi no Ryuu or Dragons of Earth or Seven Angels ("minions" in some translations) who decide that it is too late for salvation, and strive to bring about the end of the human race so the earth can be born anew. In the beginning, the two factions are missing the key members, their leader, or the "Kamui". For the Seals, their "Kamui" means "the one who embodies god's majesty", while the Angels' "Kamui" is "the one seeks god's majesty"-- giving more emphasis to the fact that both sides are fighting each other.
These two positions are open for Fuuma's childhood friend, Shirou Kamui, to fulfill, and he must choose one side. He eventually sides with the Seals and become the one similar to god. Things are not so simple though, as whatever side Kamui chooses, his twin star or shadow or other self will be forced take the enemy's. And guess who his twin star is? Yep, Fuuma. Because of Kamui's choice, Fuuma becomes "Kamui"-- the so-called dark Kamui.
What does Fuuma do once he had gained his position and received his new name? Kill his sister Kotori first and foremost as a sacrifice, supposedly to show the earth that judgment has come, and to alert his Dragons to assemble. He moves to kill Kamui next, but is stopped by someone who possesses Kotori's corpse. He realizes that this person is to be one of his Dragons, and seeks him out. With Kakyou the dreamgazer (someone who sees the future in their dreams) in his arms, he meets the rest of his Dragons of Earth in Tokyo City Hall, and applies himself as their "Kamui", and becomes very successful in leading them, while Kamui himself still flounders in his new role. This leaves the Angels free to destroy the many kekkai or the spiritual barriers protecting the foundations of Tokyo, and if they are successful, they can destroy Tokyo itself, the kekkai of Japan. And Japan is the kekkai of the world. Once Japan disappears, so will the whole human populace.
The reason, oddly enough, is fairly simple. One of Fuuma's awakened powers is to "read" or know a person's wish just by coming across them-- and even grant them. He can read any wish, but only grants the "true wish", or that one wish a person desires most, consciously or unconsciously to be fulfilled, regardless of how it may affect them or society around them. Fuuma may be granting some of the wishes he comes across, but to him, there are only two true wishes he goes off of, one of which is the earth's wish- to be destroyed, and be born again, and Fuuma takes this responsibility upon himself, helped by his Dragons. The other one, and the one almost as important as his, is the realization of Kamui's wish. He wants Kamui to realize his own wish-- which is yet unknown, even to Kamui himself, as Kamui believes that his true wish is to get the Fuuma he had known back. And apparently this is wrong.
He (sometimes accompanied by some of his Dragons) meets Kamui and the Seals several times over the course of an undetermined number of months, always doing his job of destroying the kekkai in various districts of Tokyo. Kamui, of course attempts to stop him and call Fuuma out, but he fails every time, sustaining extensive injuries after every meeting thanks to actions that can be likened to physical and emotional torture.
Some of his other more notable meeting with the Seals are with Sumeragi Subaru the onmyouji (practioner of Japanese esoteric cosmology), of whom he removes his right eye, as it is Subaru's unspoken wish to be like a certain someone from his past, and Nekoi Yuzuhira, the first and only person so far to make him retreat.
Of course, what is a war without casualties? Aside from the numerous deaths of civilians caused by the "earthquakes" resulting from the destroyed kekkai, both factions lose some members. Subaru squares off one last time against Sakurazuka Seishirou, an onmyouji-slash-assassin and Dragon of Earth, the very person from his past. Subaru kills Seishirou, and after learning a secret from the man (a whisper in his ear that most likely goes along the lines of "I love you"), he leaves the Dragons of Heaven without a word. Fuuma catches up to him, and presents Seishirou's remaining eye in a tube, stating that it's Seishirou's dying wish to give Subaru his eye, and that when he had learned that Fuuma had removed Subaru's eye, he had gotten jealous- only Seishirou had the right to hurt Subaru. Fuuma also adds that since Subaru is the killer of Seishirou, he should be his replacement, as per the laws of the onmyouji practices. The former Seal accepts because of his connection to Seishirou, and becomes one of the Angels.
Another one who goes to Fuuma's side is Kishuu Arashi, a miko (priestess) wielding a sword in her left arm. Fuuma does not have a direct hand in this though, as Arashi falls to deception by a traitor in the Seals' stronghold- Hinoto, the dreamgazing princess who had gathered the Seals for the first time around Kamui. She replaces Nataku, an artificial human, whom Fuuma had killed in order to grant his wish of dying for his most important person, by the one he loves the most. In Nataku's eyes, Fuuma is his adoptive father, and thus is the one he loves above all else, and Kasumi Karen, a Dragon of Heaven, is his "mother", his most important person.
Eventually, almost all the kekkai in Tokyo are destroyed, and when the two groups gather at the base of Tokyo Tower, the Final Battle between Kamui and "Kamui" begins. Kamui, not learning from his previous meetings with his counterpart, allows his feelings for his best friend and his confusion in learning that he has another "true wish" to get in the way, leaving him lying on his back, with "Kamui" towering over him with the Shinken pointed at his throat.