X3 opens with the members of the community attending the funeral of Fuuma and Kotori's father. As each of them come to terms with the tragedy, Fuuma, Kamui, and Kotori remember events in the past that have caused them equal grief. For Fuuma, it is holding his father in his arms as he died. Kamui remembers the dying priests prophetic words, and the devestation that Kotori felt at learning of her father's death. Kotori, sobbing in her room, remembers her mother's death. (What she can remember.)

Meanwhile, Hinoto has lapsed into another dream, floats through space until she sees a large glass egg. Inside the egg is the sacred sword, as she touches the egg, the sword becomes two, and she hears footsteps behind her. She turns and sees two Kamui's. Both Kamui's step up to the eggs, which shatter, and they take the swords into their hands. Out of their backs come wings, one with white angelic wings, and the other with black bat wings. The two Kamui's begin to battle each other, Hinoto is wounded, and they disappear.

Elsewhere, Kanoe has also seen the dream that Hinoto has, and informs the others that the sacred sword has been stolen. Satsuki then interfaces with BEAST, she then informs Kanoe that a boy with a bloody hand and flower petals imprinted on his forehead was seen carrying a long, cloth wrapped object. Kanoe acts very surprised.

At Togakushi, Sorata tracks down Kamui and confronts him about his destiny. Unfortunately, Kamui wants nothing to do with this, that is until Sora tells him that he is one of the seven Dragons of Heaven. He then proceeds to tell Kamui about his childhood before he found his destiny, most of which he can't remember. At which point, they realize that they are being watched.

A young woman stands in the rain before them, and to their surprise, reveals that she is Kamui's aunt. Tokiko is her name, and she takes both Kamui and Sora to her house to tell them about Kamui's family. Kamui can't get over the fact that Tokiko looks remarkably like his mother.

Back at Togakushi Arashi watches the mourners come and go, all the while remembering what Hinoto has told her, and asking her to protect Kamui. Feeling somebody watching her she whirls to face a man staring at her. He seems surprised that she noticed him. Before she can confront him, they are surrounded by Men in Black. Arashi lookes through her hands (puts her hands together in a pyramid shape) and sees that they are Curse Zombies. She quickly puts up her kekkai, only to be shocked when she finds the man from befroe inside the field. The zombies don't really care and attack them both. Arashi unleashes the sword from her palm, and retaliates, unable to figure out why the man is so calm.

As the zombies rush to attack him, Arashi tries to get to him, but he ends up unleashing powers of his own, the power over wind. The two quickly defeat the zombies, after which he informs Arashi that he is Aoki Seiichirou, and he too is one of the Dragons of Heaven.

At Tokiko's Sora and Kamui feel the power of the kekkai, Sora pinpoints the kekkai at Togakushi. Kamui rushes out, fearful for Kotori, with Sora quickly following. Tokiko tells them to come back soon.

Seiichirou's pocket beeper rings, and he rushes off, but not before giving Arashi his umbrella and his card. Arashi vows to meet him again, only to turn and see Kamui and Sora watching her from a nearby telephone pole. Kamui recognizes her as the girl who took Saiki from him before and angrily confronts her. Sora jumps in and tries to calm things down. Arashi thens informs them of her mission, and that there was another member of their team there a minute ago, but he was called away by his beeper.

Sora tries to break the tension by teasing Kamui about Kotori, then suggests that they head back to Tokiko's, inviting Arashi along. They arrive at Tokiko's, which has now become a burning ball of flame. As Kamui stares into the fire, he is confronted with memories of his mother's own fiery death.He tries to jump into the fire to save his mother, Sora stops him, and Arashi informs them that there is no human in the fire. They turn to leave, unaware that someone is watching them. A scantily clad woman sits atop a telephone pole. With a short giggle and a flurry of feathers she vanishes.

Back at Togakushi, Fuuma has fallen asleep. In his dream he sees a glass earth, and inside is Kanoe. Kanoe asks him to save the earth, and the scene shifts to a scene from his childhood where he, Kamui, and Kotori happily play together. His mother enters the scene and leads the children away. From behind him he hears a horrible scream. Suddenly he is inside Togakushi. Running to a nearby room he is greeted with the horrific site of his mothers dimembered body. As he stares in horror a boy appears before him. It is Kamui, who pick's up Fuuma's mother's head and licks the blood from his hands.

The scene shifts once more and his father is pointing towards the ruined city of Tokyo. His father's chest explodes with blood, and the scene shifts once more. This time to his horror, Kotori is crucified to a large steel cross. Wires cutting into her flesh and tearing at her skin. The Kamui with bat wings appears, and to Fuuma's horror, impales Kotori with the sacred sword. The scene shifts and Kanoe explains to him that the only way he can change the future that he has seen is to kill Kamui. Fuuma wakes from the dream with her terrible prophecy echoing through his mind.