In the manga version, Monou Kotori was born as the second child in the Monou family from the Tokagushi shrine in Tokyo, two years after her older brother Fuuma. Since always, Kotori had a weak heart and a very frail health, like her mother Saya, and was very prone to fatigue and collapses, so she was permanently under tratments (in fact, the time Sora and Yuuto fought in the Tokagushi temple, we see Fuuma reading a file with the medicines that Kotori should take). 

A beautiful woman named Shirou Tooru used to visit the temple very often, bringing her little son Kamui with her. So it was natural for Kotori and Fuuma to play with Kamui while Tooru and Saya (which was Tooru's friend since childhood too) talked about life. It was then when Kamui made a promise to her: that when they gre older, he'd protect her and Fuuma no matter what. 

All of a sudden, everything was over. One afternoon, the Monou kids and their father Kyougo (the owner and priest of Tokagushi) found Saya's corpse torn into pieces, alongside with a mortally beautiful sword. The Shinken (God Sword), which Kyougo swore to protect, not telling the children why. 

Kamui and Tooru didn't come back to the Tokagushi shrine since that day.  Kotori grew up very lonely, but pampered by Fuuma and Kyougo, while sweetly waiting for "Kamui-chan" to come back. 

And when Kotori turned 15... suddenly, she started to have strange dreams. Always with somethig in common: a beautiful boy looking very alike her Kamui-chan. She didn't know it, but her power as a DreamGazer was starting to unfurl. 

As she dreamed, Kamui came back, though a lot different than the boy he used to be. He rejected to see her and Fuuma saying that he'd only bring trouble. And her dreams changed: they always talked now about herself being killed, in different ways. 

That was when Kyougo, the Monou father, was murdered by a strange boy in Chinese clothes, using a stole as a weapon: Nataku.  It (?) stole the Shinken and fled, mortally wounding Kyougo.  Not only Kotori did take it very badly,but another death follows: the one of Tokiko, Kamui's aunt (Tooru's younger sister), who gave birth to the second Shinken just like Saya did. Upon seeing the woman dead in the same way her mother died, Kotori's sanity shatters, and she goes insane. 

In the following dream, Kotori nearly died (her heart slowens critically), and she finds Kakyou who tells her to come back to life. He can't, however, rescue her mind totally, so Kotori definitely is mad. She goes with Kamui and Fuuma to CLAMP campus (by request of Nokoru Imonoyama, the chairman), so that she's protected while Kamui takes his Shinken there.  BUT... 

While Fuuma is telling them that he decided to protect Kamui, the Dragon of the Earth ends up possessing him and his self.  Kotori, who's playing around a fountain there, is captured and tied up with wires to a metalic cross. Fuuma impales her with the Shinken, then rips her body apart as the cross falls apart too.  All the while, a gravely hurt Kamui couldn't do anything... 

However, someone has been able to help Kotori. That one is Kakyou. He possesses Kotori's body enduring her physical pain, and later says goodbye to her spirit as she flies to Heavens and disappears, telling him that she loved Kamui and Fuuma and (the most important) that the future's still undecided, not foreordained.
 

In "X:The Movie", Kotori also has dreams about Kamui's return, and she tells them to Fuuma at night (apparently in this movie, Kotori isn't sick, and Kyougo and Saya died years ago so Fuuma has raised Kotori by himself).  While they're going to close the Tokagushi shrine, they're attacked by Satsuki's BEAST (manipulating wires), but Kamui comes to the rescue. 

There's a little talk (with Hinoto's first appearance towards Kamui in between), and it starts to rain. However, it's raining ONLY in the temple. Nataku and Shougo Asagi (who replaces Kakyou in the movie) appear to take Kamui to Kanoe's presence. The Dragons of the Heavens in assembly (sans Subaru, who killed Seishirou and died in the process) come and fight.  However Kanoe, by casting a spell, kidnaps Kotori, and Fuuma is pulled also into while trying to rescue his sister. 

The movie progresses (Fuuma turns evil, Nataku and Seiichirou kill each other, the same for Karen and Shougo), but Kotori is mostly trapped inside of  Kanoe's dream, while dreaming herself. Kamui, who is investigating in the temple after a talk with Hinoto, is pulled into her dream and sees her whispering: "Kamui... What's this?  It's gonna be born... soon...", and as she opens her eyes, she dies.  That vision makes Kamui decide to go with the Ten no Ryu. 

We don't get more of Kotori (meanwhile Fuuma fully awakens as a Chi no Ryu, Yuzuriha is killed by Yuuto, Sorata is hurt, etc.), who's still in Kanoe's dream. After killing Kusanagi and reveal himself to Kamui (who's saved by Hinoto), Fuuma forces Kanoe to take him to Kotori's presence. He awakens Kotori and says: "There are two Swords of God. One is yet weilded by Kamui, the Dragon of the Heavens. And this one...", he puts his hand over Kotori's belly, "is for Kamui, Dragon of the Earth". 

A terrified Kotori tries to flee from Kanoe's dream. Kamui guides her with the help of Hinoto, so she comes to the Diet Building where the remaining Dragons of the Heavens are and will help her. As she arrives, however, she's captured by Fuuma, who strikes her and with his bare hands, pulls the second Shinken (Toru, at the beginning of the story, gave birth to the first one, who's in Kamui's grasp) out of Kotori's body, killing her in the process. 

For a long while, Kamui is unable to react, holding Kotori's corpse in his arms. Then Fuuma (after killing Yuuto and Satsuki) reappears bringing Kanoe and kills her in front of Hinoto herself. Sorata and Arashi carry Fuuma outside of the Building (while inside of Sorata's kekkai), but Sorata is killed, and so is Arashi while she was morning for him (UNFAIR!!! TT).  Hinoto, with her last remaining power, sends Kamui and the dead Kotori to the Tokyo Tower, and dies crushed under the Building with Kanoe's corpse in her arms. 

Kamui tries to convince Fuuma to give up, but is unsuccesful. He realizes and spreads his kekkai, and fight Fuuma after he lays Kotori in a platform. Finally, Kamui makes his choice... and kills Fuuma as he cuts his head off. While he mourns Fuuma, his friend's head in his arms, Kotori's body is surrounded by white feathers, while in the screen we get the replay of Fuuma's promise: "Ah, so you remember the vow. You promised before leaving that you'd be back to protect Kotori. Well, I made a vow too: if you come to protect Kotori... Then, I will protect you!". 

Kamui, crying, says, in the last line of the series: "Fuuma... You... But why? Why does it have to end like this... Answer me!...