X9 opens with the Kamui screaming at Fuuma, who relies that there is now another Kamui. He goes to remove the sword from Kotori's body when she grabs the sword and Kakyou reveals himself to Fuuma. Fuuma asks him if he is a Yume-mi, and then realizes that Kakyou is a Dragon of Earth. At the same moment the Dragons of Heaven arrive at the campus and stare in horror at the scene that spreads out before them. Fuuma turns and stares at them, half-amused. Kotori feebly tries to push the sword from her body while Kamui stares numbly forward, still pinned to the upturned floor with glass. Seiichirou tries to shield Yuzuriha from the bloody scene. As Fuuma leaves to find Kakyou, the cross falls apart and Kotori's body is ripped to peices by the wires that were holding her there. Sorata yells for Kamui to stay put, but Kamui rips himself off the floor, staggering forward until he can get free of the pole stuck through his leg, and collapsing near Kotori's head. Because Kamui could not use his powers to save those that he loved, his heart and mind shatter, and he lapses into a deep trance.

Hinoto cries for Kotori and for the pain Kamui is feeling, while Kanoe is chilled with the power that Fuuma has displayed.

Inside their dream, Kotori thanks Kakyou for sparing her the pain of death. As angelic wings spread from her back, she kisses Kakyou goodbye, then tells him to tell Kamui that the future is not yet decided, and that she loved both him and Fuuma. Kakyou sadly watches her go and then turns towards his dream of ruined Tokyo.......

Deep in CLAMP campus, a freshly bandaged Kamui sits and watches nothing. His eyes completely dead, he holds Kotori's head in his hands, not hearing Sora calling to him, desperately trying to snap him out of his trance. Outside the room the Dragons of Heaven wait for word on Kamui. Seiichirou quietly holding the sobbing Yuzuriha. As Sorata enters the room Arashi jumps up and asks him about Kamui's condition. Ufortunately it doesn't look good, Kamui has retreated into his own heart, and doesn't want to come back and face reality.

Trying to decide what to do, it is Subaru who finally decides to take action. He goes into the room where Kamui is resting and sits down next to him. Arashi is alarmed when she realizes that Subaru is going to enter Kamui's "muddy conscious". But Subaru reassures her, and after a few incantations is pulled into Kamui's mind.

Inside Kamui's visions, he is attacked my a dragon, but knows he cannot fight back because it might damage Kamui. He finally makes it past, and sees Kamui, Kotori, and Fuuma standing in the fountain at CLAMP Campus. Fuuma once again attacks Kamui (as we saw earlier in X8) but instead of getting pinned down by Fuuma with glass shards and steel poles, Kamui is held back by a manifestation of himself which grins evily at him. And then, as Kamui looks on in horror, yet another version of himself jumps onto the cross and murders Kotori. He rushes to catch her head. Once he catches it he falls to his knees, the floor turns into liquid and he and Subaru are pulled deeper.

This time it is an earlier childhood memory, seemingly sweet with the trio (Kamui, Kotori, Fuuma) playing with birds near the shrine. As they run off, Fuuma starts to lag behind. Kamui turns back to help him catch up when Fuuma's face starts to bleed. Kamui stares at his friend in deep concern which quickly turns to horror when adult Fuuma appears and kills the younger version of himself. Kamui turns to shout a warning at Kotori, but finds he is too late as she is killed by adult Fuuma with the sacred sword. Kamui screams as Subaru sadly looks on.

Meanwhile at the Four Seasons Hotel, Fuuma has arrived. He blasts a hole in Kakyou's room wall and enters, but as he prepares to pull back the curtain behind which Kakyou lies, he is pulled into a dream. We see Kakyou, in his non-imobile form, sitting on a sphere. Fuuma asks him his name, and then if this is his dream. Kakyou doesn't reply but points to the floor where an image of the child Kamui appears. A glass feather lands in Kakyou's hand and a replay of Kotori's last words are shown to Fuuma. Fuuma tells Kakyou that she was wrong. The future is decided, and there is only one. He then rips the dream apart and we see Kakyou lying in bed, surrounded by medical devices and IV-units.

Inside Kamui's mind Subaru kneels beside the little boy to listen to him, gently at first, and then angrily when Kamui refuses to listen. Kamui asks him who he is, and Subaru answers. Kamui then begs him to save Kotori and Fuuma, who's bodies are rapidly dissolving into cherry petals. Subaru tells him to listen to him, for he knows Kamui's pain, although it is slightly different. We then see an image of Hokuto (Subaru's sister) walking in sakura. Seishirou appears before her and then kills her. Kamui starts to run towards them, but Subaru stops him, telling him it is only a painful memory of the past. Kamui will never probably fully heal from the pain, but there is always hope for the future, and this is why Kamui must fight. Kamui smiles at Subaru, and then grows to his present age, he tells Subaru that no matter what, he still cares for Fuuma and wants to get him back.

Back at Four Seasons, Fuuma asks Kayou to go with him. Without much choice in the matter Kayou agrees. As Kayou leaves with Fuuma, Subaru pulls Kamui up from the inner depths of his mind, and for a moment, the two dreams collide. Fuuma and Kamui are thrown face to face. Kamui stares at Fuuma and then reaches out towards him. Fuuma looks at him coldly and then turns his back and walks away.

Back at CLAMP Campus, while the Dragons of Heaven look on anxiously, Kamui awakens with Subaru. Kamui thanks Subaru, who smiles and then collapses, exhausted. Sora yells for Arashi to call a doctor, and she quickly runs off. Kamui turns to look at Kotori's head and whispers her name as a single tear escapes and slides down his cheek.

Meanwhile, Fuuma and Kayou have arrived at the Tokyo Govenrment offices.

Back at CLAMP Campus students rush off to classes, unaware of the situation at hand. In a nearby park-like area Kamui stands underneath a large cherry tree, underneath which Kotori is buried. As he stands lost in memories of the past, Sora quietly joins him, explaining to Kamui that he is sorry that there was nothing he could do, and that they got there too late to help. They are soon joined by the others, and then one more.

Sitting in the branches of the tree is a beautiful woman. She introduces herself as a Dragon of Heaven, Kasumi Karen. After the others introduce themselves, and they learn that Karen works for a "soaphouse" (where Seiichirou has been before). Karen delivers a final message to Kamui from Tokiko. Soon after which, the CLAMP Campus detectives arrive and tell Kamui to bring the sword. There is someplace they need to go.

Deep under the Diet bulding, Hinoto is lost in a dream with Kakyou. They argue for a moment about Hinoto's real dream, and then Hinoto sees them approaching the Tokyo Government offices. Deep under which Kanoe sits dreaming. Hinoto screams for them to stop as someone lays their hand on Kanoe's shoulder, she is violently ripped from the dream. Hinoto awakens crying. As Saiki, Sohi, and Hien rush to her aid she pulls away from them, whispering to Kakyou.

At the end of X9 there is a special story about Kusunagi. It is a continuation from Yuzuriha's story in X6. Kusunagi has bought her a crepe, and they walk down the street happily. Kusunagi tells her he is glad she stopped crying, and that she scared him earlier when she suddenly burst into tears. There is then some discussion about Kusunagi's ability to feel the pain of the earth.