Kazuki Azuma returns to Japan after ten years away, only to be chased down by the Bubuki police. He's saved by a childhood friend, Asabuki Kogane, and her right-hand-shaped Bubuki. He then meets the Bubuki users Nono Hiiragi, Ougi Kinoa, and Taneomi Shizuru. Azuma has never even heard of Bubuki, but after learning that he's the user of the "heart" Bubuki, he makes his way to the Buranki prison in Shinjuku's underground to awaken the sleeping Buranki called Oubu.
Azuma stares in stunned shock at Oubu, now reduced to bones, as Hiiragi, Kogane, and the others successfully hold off Matobai. Hiiragi realizes this is the best chance to awaken Oubu and demands the heart Bubuki from Azuma, but Azuma insists he has no such thing. Believing that the heart Bubuki will react if its owner is in danger, he attacks Azuma with Iwatooshi!
Ten years ago, many Buranki fell to Earth and were destroyed by Banryuu Reoko and her Buranki, Entei. That was the day Reoko and Entei's reign of terror began. In the present, Azuma and his companions flee Shinjuku and meet a woman named Horino, who tells Azuma that his mother was the only person who ever defeated Reoko. She then tells him there's more he should know, and leads him to the "Kazuki library."
Kogane's enraged cry of "I'll gouge out your everything!" rings out as she engages Matobai in battle, but her opponent's attack power overwhelms her. When Azuma tries to help her, Matobai mercilessly fires his Bubuki gun at him, but the heart Bubuki shields him. Azuma tries to use the heart to call Oubu to fight, but it doesn't respond... and Matobai sneers at their confusion as he takes out Entei's heart Bubuki.
The Bubuki battle continues aboard the train that's carrying Oubu toward Treasure Island. A beam fired from Arabashiri's Bubuki ring hits Kinoa, causing her own past to replay in her mind and slow her down. Azuma tries to help, but Kinoa stops him, saying she must settle her own score with Arabashiri. So Azuma agrees to just watch, but Hiiragi can't help wondering what Kinoa's relationship with Arabashiri is. What really happened in their past?
Azuma's companions have won their second Bubuki battle, but the next opponent is one of Reoko's Four Gods who was in disguise as their friend Horino. Hiiragi and the others are shocked to learn that their trusted friend is actually working for their mortal enemy. Kinoa demands to know why she betrayed them, but Zetsubi easily dodges the question; Hiiragi attacks her in rage, but he's no match for the power of Zetsubi's Bubuki. Azuma's suggestion of figuring out what the opponent's Bubuki's power is momentarily calms Hiiragi, but soon enough...
When Azuma sees the Buranki approaching the train that's transporting Oubu, he recognizes it as the headless Buranki that attacked his family on Treasure Island ten years ago. Frozen in place, it seems Azuma is about to be trampled underfoot, but Kinoa saves him in the nick of time with Hoemaru and Himekiri. The relieved Kogane joins them along with Hiiragi and Shizuru, when the four Bubuki come together, the heart in Azuma's hand radiates an intense light in concert with a shining beam emitted by the skeleton of Oubu.
The only two Buranki currently on Earth that possess a beating heart are Oubu and Entei. What's more, Reoko has defeated the headless Buranki, also called the "déraciné," and obtained its heart. One man declares this a situation that cannot be overlooked, and sends several Bubuki users to Japan in order to reclaim the stolen heart. Meanwhile, as Azuma and his companions continue to ride the Buranki transport train, a man carrying a guitar shows up in front of them and forces Hiiragi to slam on the brakes. Just who is this man?
Azuma does everything he can to restart the heart of Oubu, which stopped beating during the battle with the American Bubuki users. Hiiragi tries to protect Azuma from a vicious attack, but ends up sent flying and crashes to the ground. The American Bubuki user Luis commends Hiiragi for risking himself to save his comrade, and criticizes Azuma for just letting his friend protect him. Epizo stops Luis and declares that the two team leaders should settle this score together, and faces Azuma with fists at the ready.
As Oubu finally achieves its complete form, Entei stands before it controlled not by Reoko, but by Zetsubi. Laughing boldly, she tells the shocked Azuma that he can't beat Entei, but Kinoa insists that they and Oubu are different from before. Zetsubi is cornered by Oubu's ferocious attack, so she takes the Russian team's Bubuki to use as Entei's limbs, and Oubu is overwhelmed again. Can Azuma and his party win this fight?
The foreign teams continue to hunt the headless déraciné Buranki, so they can take its heart and use it to awaken Buranki in their home countries. Meanwhile, Arabashiri is fighting his own battle for Reoko's sake. He has watched Reoko endure the ceaseless pain of fighting déraciné Buranki one after another with the incomplete Entei, and now his rage explodes on Azuma's mother, Migiwa.
As Reoko, full of bitter resentment, grasps Migiwa in Entei's hand to try to crush her, both women look back to when they were sixteen years old and best friends. Reoko called forth Entei in Ueno to bring the long-buried existence of Buranki to light, but Migiwa burned Entei's limbs to stop this uprising, which left Reoko's body with the curse it still bears today. Why did Reoko decide to walk a path of blood after she was released from her years of confinement? Their hidden past is finally revealed.
Half a month after the battle on Treasure Island, Kogane, Kinoa, Shizuru, and Hiiragi ride through the lively streets of Taiwan in a taxi... but Azuma got stuck in immigration and had to catch a later flight. The girls are thrilled by the sights of their first visit to Taiwan, but Hiiragi reminds them that they're there to find the body of the Buranki that went missing when Treasure Island fell. Just then, a headless Buranki shows up at the airport where Azuma is soon due to arrive...
Guy praises Leticia for destroying most of the headless Buranki lurking around Europe. This irritates Kaoruko, who wants Guy to acknowledge her as the number one heart user. Then, when Kaoruko finds out Maxim was given a special mission, Guy tells her that she must first demonstrate her talent as a heart user. Still, Kaoruko boldly laughs, convinced that she will be the one to protect the world with Oubu.
As Azuma and Kaoruko stare each other down, their respective limbs battle it out with their Bubuki. Angus is on the defensive against Kinoa's fierce attacks, Shepherd is overwhelmed by Shizuru, Joan can't get a single attack in against Kogane, and Lakshmi struggles against the cooperative relationship between Hiiragi and Iwatooshi. As the members of the Asian team, who have been under the complete control of their leader Justin, watch the Japanese team fighting without being tied down by their leader, they start to show signs of changing...
The Buranki Entei flies freely through the sky... and the one controlling it is not Reoko, but Kaoruko. Demokratia, led by Guy, has used its technology to make Entei recognize Kaoruko as Reoko. Guy then tells Kaoruko that there is a traitor among them in Demokratia, but she's unable to conceal her shock when told that the traitor is a fellow Bubuki user and ordered to eliminate them.
In a room somewhere deep in Demokratia's island fortress, Kaoruko discovers the identity of the Bubuki users that Guy had called "traitors." She asks Double why she never knows what's going on and why all this happened, but Double only tells her that if she doesn't live up to Guy's expectations and eliminate the approaching Azuma and Oubu, she'll receive the same treatment as the traitors... and that there are some things she doesn't need to know.
Kaoruko has been trying to find a way to see her father again ever since he left her at a boarding school in Taiwan. One day, Guy tells Kaoruko that her father reunited with her mother by going up to Treasure Island in a Buranki that still had its brain. Sensing that Kaoruko, despite her brave act, really wants to see her parents again, Guy makes a proposal that will allow him to use her feelings to serve his purposes...
Peaceful scenery passes by outside the car window, but Azuma has no idea that the kind old man giving him a lift toward the island fortress is Guy himself. Meanwhile, back at their hideout, Kogane and the others are being attacked, and Matobai and Tsuwabuki realize that Azuma is gone. Hiiragi and Kinoa say that until he comes back with Kaoruko, they're on their own, but Matobai's subdued gaze is fixed on the Buranki Batolov.
The Buranki Epimew soars over hills and plains, faster and lighter than the wind, disappearing from sight in an instant only to rise high into the sky again. In the cockpit, Laetitia is delighted by the sight of whooper swans flying by. Since she lives her life in a wheelchair, the world as seen from the birds' point of view is wondrous to her. Epimew flies past the birds and shoots high above the clouds, higher and higher. What's going through Laetitia's mind as she finally reaches the heights of space?
After rescuing Reoko from Guy's island fortress, Azuma and the others rest of the Japanese crew flies back to Japan... but the moment they're over Japanese waters, a flying craft approaches at high speed. From the heart waveform, Matobai determines that it's Mega-lala. Azuma leaps out to the hull of their flying boat to face the Buranki, and a battle between two heart users who could have been great friends if not for the involvement of Bubuki and Buranki begins.
Inheritance: if one were to express it with a different word, it would be "curse." Guy, an inheritor of a heart Bubuki, was released from the curse through the only possible method... only to have it return to him in a sudden turn of events. In anguish, Guy made up his mind to eliminate from this world all the Buranki that had tainted human blood and placed this detestable curse on them, thereby returning the world to untainted human hands. Now, 16 years later, everyone watches the sky as a huge comet approaches Earth...
The massive Deus Magna seems to pierce the heavens as it makes its appearance amidst a raging storm, and inside its cranium is the enemy, Guy. The Buranki Batolov and Mega-lala, along with Zampaza piloted by Kaoruko, wield the Bubuki from Laetitia's fallen Buranki as they charge forward to stop him, each for their own individual reasons. But no matter how fiercely they attack Deus Magna, they can't even leave a mark. Meanwhile, inside Deus Magna's body, Azuma and his team enter the battle with Oubu to try to stop Guy and save Reoko.
It's been a year. Peace has returned, and everyone is back to living their old lives again. Azuma has started living on his own and now attends the same high school as Kogane. All Buranki controlled by Guy's Demokratia have been handed over to government-managed companies. As he watches the news over breakfast and opens a letter from Epizo, Azuma can't help but feel how much quieter his life is now.