During the last days of the war, Emperor Arthur Gaz orders one of his official to be in charge of a secret project codenamed Chaika. A month after the events of the Soara, Toru, Akari, Chaika duels with Lady Claudia Dodge, another of the Eight Heroes and her men but Chaika loses to Claudia. Despite this, Claudia allows Chaika and her companions to stay at her estate.

As Chaika, Toru and Akari try to find a way to beat Claudia, elsewhere, Red Chaika and her group defeats another Hero, Glen Donkervoort, acquiring Arthur's right arm and heading towards an island as suggested by their informant Guy. Eventually, Chaika manages to shorten her spell and defeat Claudia after the latter is distracted by Fredrika in her cat form. Claudia congratulates the group by hosting a tea party to celebrate. Meanwhile, Konrad's secretary Karen Bombardier gives Vivi Alberic's investigation notes on Emperor Arthur before rejoining the Corps with Alberic's sword in hand. Back at Claudia's estate, she reveals to Toru's group why she has no interest with Arthur's remains and gave hers to Chaika and tells her secret. During the end of the war, the Eight Heroes learn one of Arthur's officials escape with Arthur's hidden fortune and most of his magic research work to a secret island, and despite the Council attempts, they could not find the island or Arthur's magic research. After giving Toru group the location of the Heroes, Claudia bid them farewell. Soon Toru's group learns Red Chaika has already claim one of Arthur's remains from Glen while Chaika wants to find the secret island to learn about her origins.

Arriving at a seaside town ruled by Clay Morgan of the Eight Heroes, Toru and group disguise themselves as a comedy troupe to enter Clay's mansion. When Clay learns the groups attentions and sees Chaika, he runs away screaming while Toru and Akari chases him. Chaika tries to find clues of where the secret island is which she finds a lead at the Evil Sea. Toru and Akari find and defeat Clay, learning he's been scared of Emperor Arthur after fighting him and Chaika since she was beheaded by the leader of the Eight Heroes, Stephan Hartgen, so he gives up Arthur's ears so he won't have to see Chaika or the remains again. After acquiring Arthur's ears, Guy appears and tells Toru and Akari to head to the secret island but both of them are now wary since Guy knew about the other Chaikas. Meanwhile, Shin informs his master Stephen that all of Arthur's remains will soon be arriving which Stephen promises his daughters Irina and Alina they will get to see it. Meanwhile, Toru and Chaika have an argument as the latter wants to find the secret island which the former refuses believing it's dangerous which leads her to firing Toru. After Akari convinces Toru to make amends with Chaika, they learn too late that Chaika has left to find the island with Fredrika. Both of them chases after her on Clay's ship where Red Chaika and her group have sneaked in but the ship is sunken by a Kraken. Chaika and Fredrika finally found the secret island but are attack by dragons.

Chaika arrives on the island where the emperor's fortune is said to exist, but she's quickly attacked by a pack of Orthros, followed by a group of demihuman soldiers.

The two Chaikas are captured again. The red Chaika says they should work together just this once to escape, but as they search for an exit, they find a girl confined in a hidden office. She introduces herself as Niva Lada and says she's been waiting for Chaika.

As Toru and his companions head to the Principality of Hartgen to get the last of Arthur's remains, the Gillett Corps arrived at the Secret Island and learn from Kiril and Ursula what happened on the island before they arrive. At Hartgen, Red Chaika and her companions enter the tournament after defeating other contestants in the preliminary rounds. Toru and his companions also enter the tournament as well, in order to win Arthur's remains should they fail to steal it. Zita and Matthäus meet with King Stephan in order to convince him to cancel the tournament but to their shock, not only do they discover the King's daughters, Alina and Irina, are also Chaikas, but the King refuses to cancel the tournament. Meanwhile, Vivi and Nikolai enter the tournament as well where they are shock that the tournament allows the contestants to kill. Guy visits Alberic, whom latter is revealed to have lost his memories, that Guy rescued him because of the hatred in his heart. As most the contestants rest for the night, Toru and Akari attempts to sneak in the King's castle to steal the remains while Chaika sees Niva leaving with Guy voluntary.

Toru and Akari attempt to infiltrate the castle in order to steal the remains but their mentor Shin appears, forcing them to escape. Meanwhile, Guy brings Niva to Stephan Hartgen, who is eager to start a new war, as he believes that warriors like him can be only worthy in combat. In the next day, the tournament begins, and while facing other contestants, Toru and Chaika meet Vivi and Nikolai, but instead of fighting, they decide to share information instead, and learn about the two Chaikas that are always beside Hartgen. Little they know that the two Chaikas answer to a third one, who has her own agenda. As the Council of the Six Nations discuss if they should launch an attack on Hartgen, Konrad is informed about the situation there while the pairs composed of Chaika and Toru, Boghdan and David, Akari and Fredrika, and Vivi and Nikolai advance to the next stage of the tournament, oblivious to the fact that Stephan is aware of their presence and is making arrangements for them to fight each other.

Toru and Chaika have advanced through the tournament and made it inside the third castle wall, but then they're captured and ordered to proceed to a different arena. Seated inside waiting for them is the black Chaika, who says this is where they will atone for their sins.

As Toru, Akari and Fredrika are kicked out of the castle, Red Chaika decides to give her remains to Chaika's group only to learn from Selma that Hartgen's men attack and stole if from her. Zita and Leonardo reunite with Vivi and Nikolai and learns Alberic is alive. With Fredrika weaken by Shin's poison, Toru and Akari have no choice but to give the rest of the remains to save Chaika. After informing his superiors on what happened, The Gillette Squad are ordered to take down King Stephan before any of the Six Nations attack, which will reignite the war. Toru and Akari arrive in Stephan throne room where Stephan, Alina, Irina, Black Chaika, Niva, Guy, Shin and Chaika awaits them with Alberic sneaking in. With all of the remains gathered, Black Chaika "consumes" the remains and starts giving birth with Guy's help, who reveals he is a magic mechanism to ensure the remains would be gathered. Black Chaika gives birth to a boy resembling Guy but with Fayla body parts who reveals himself to be none other than Arthur Gaz himself. Arthur thanks Black Chaika for using Fayla parts in her to resurrect him and kills Stephan with a spell without an incantation much to everyone shock. As Arthur sits on the throne and grows older, he explains to Chaika the truth that she and her "sisters" were never really his real daughters as the Chaikas were based on his mistress who was killed by Stephan during the war which he uses as a basis for all of the Chaikas looks. Arthur reveals his goal was to gather large amounts of magic fuel using several flying fortresses hidden in space to collect from people's emotions with war bringing out the most of their emotions. So he allowed himself to be killed and his remains scattered while the Chaikas fought to get them so the dread and fear about him would spread throughout the continent. To demonstrate his power, Arthur and Niva easily destroys a flying fortress sent to attack Hartgen.

After destroying several of the Six Nations flying fortresses, Arthur heads to one of his space fortress along with Shin to begin his plans. Toru decides to make a pact with Fredrika by becoming a Dragoon Cavalier in order to fight Arthur while Akari, Vivi, Leonardo, Red Chaika and her companions face off against Black Chaika and her minions. Assisted by Chaika and her Gundo sniper rifle to enter the space fortress, Toru battles against Shin before finally defeating him. Red Chaika faces off against Black Chaika before giving her the finishing blow, ending the latter controls of Alina, Irina, and the Chaika warriors. Finally facing Arthur, the Emperor beckons Toru to join is side since he believes war is what all of humanity wants but Toru refuses and he and Fredrika are swiftly beaten. Before Arthur can kill them, Chaika casts a shield to protect Toru and Fredsrika. Arthur tries to kill Chaika using Niva but Niva refuses and joins Chaika's side. With no more magic bullets to use, Chaika uses her memories as magic fuel for Niva's Cannon Gundo form where they finally kill Arthur and stopping his plans before Chaika loses conscious. In the aftermath, Alberic, now the new chief of the Kleeman Agency, reports to the Council of Six Nations that Arthur's plans were thwarted, Niva is under their custody and claims all of the Chaikas died. Elsewhere, Toru, Akari, Chaika, Fredrika and Red Chaika now live together where Toru helps a recovering Chaika.