Jin suddenly wakes up in an ISDA room, where he is questioned about the shuttle accident two years ago. He is also told the truth about the asteroid Thanatos, in which extraterrestrial life called Dragons came to Earth from Thanatos. Hearing that one of these dragons was the cause of the shuttle accident, he asks them to tell the truth to the public, so his father's name could be cleared. They deny his request and instead ask him to become a Dragonaut, which he rejects. He then meets Kazuki Tachibana, his old friend, who now works for the ISDA. Later, Jin remembers where Toa is to meet him, so he runs away from the ISDA to see her. The two are finally reunited, but it is cut short when the ISDA attempts to capture Toa. During their attempt, one of their own, Spirytus, transforms into a dragon and attacks Jin. In order to protect Jin, Toa reveals that she too can transform into a dragon.

Toa and Spirytus continue their battle as dragons, but once their battle reaches a critical point, the ISDA is given permission to interfere in the battle. Thus, Machina, Amadeus, and Howlingstar transform into dragons, controlled by their "pilots", Akira, Sieglinde, and Raina, respectively. Despite the odds, Toa manages to hold her own, which is when Gio, Kazuki's dragon, arrives on the scene, having previously been awakened by one of Toa's shock waves during the battle. As Gio, who is concerned about Toa, transforms into a dragon, Jin hops on his back so he can try to help Toa. As the two reaches Toa, Jin sees a vision where Toa tells him that she can no longer be with him now that he has seen her real form. Gio then shows up to tell Toa that he was created in order to protect her, and as the two were about to link hands, Howlingstar attacks them, returning them to battle. Then, Toa accidentally knocks Howlingstar onto Gio, plunging Gio and Jin into the ocean.

During an ISDA meeting, the subject of whether or not the D-Project should be made public is brought up. Meanwhile, after Jin wakes up on a beach with Gio, they discuss what Toa is to them. Jin then hears Toa singing, which he realizes is coming from the moon. Later, Machina and Akira come across Gio who is apprehending Jin, so they bring the two back to the ISDA. As Jin is being questioned by Akira, Gio explains his actions to Sakaki, the Dragonauts' military commander. When Gio is being escorted to Yuuri, he escapes, and Jin is also revealed to have escaped after being questioned. This is when Akira realizes that Jin and Gio planned their capture; in order to get a pod necessary for Jin to go into space with Gio. After Gio's brief scuffle with Machina, Akira's dragon, Gio transforms and Jin attaches the pod to Gio's neck. They then fly off towards the moon in hopes of finding Toa.

A flashback sequence shows how the military tried a Resonance program five years ago, but it ended in failure. Presently, during their ongoing search for Toa, Gio decides to abandon Jin believing that he was wrong about Toa being on the moon, not realizing that they have just missed her. Meanwhile, back on Earth, the ISDA publicly reveals the truth about the D-Project and Thanatos. The Dragonaut team is then ordered to focus on the D-Project, whilst the military handles the recapture of Gio. In the lunar city, Jin is captured by Garnet and the military. In order to lure Gio in, Garnet sends a public broadcast about Jin's capture, but in a frequency which only dragons can hear. Gio initially ignores the broadcast, but after accidentally seeing Toa in a video that some kids took, he goes to save him. During his attempt, Gio battles Garnet while being weakened by a machine, but as Jin tries to escape, he destroys the machine. Gio then saves Jin and transforms into a dragon.

During a flashback, it is revealed that Jin had been operated on after the shuttle accident, during which Yuuri, an ISDA researcher, claims to have noticed signs of a Resonance. In present time, Yuuri and Sakaki request for Kiril to reassign the Lindworm Unit to capturing the Album [Toa]. The mission is accepted so Raina, Akira, and Sieglinde travel to the Moon, where Jin and Gio continue their search for Toa. As Yuuri arrives home, she unexpectedly encounters Kō, who shows her incriminating evidence regarding Amagi. Back at the moon, in a coffee shop where Toa had been staying, she is encouraged by the owner to not deny her feelings, so she decides to go look for Jin. When she finally finds Jin and Gio, Howlingstar, Amadeus, and Machina arrive in order to capture her. Gio interferes and fights Howlingstar, and as Amadeus takes Jin to Sieglinde, Machina engages Toa, but instead of fighting, she asks Toa why they were born, to which Toa replied that it is all due to destiny.

After finally reuniting, Jin, Gio, and Toa receive tickets for a spa resort from the coffee shop owner. At the spa, Jin and Toa deepen their relationship, while Gio continues to wonder about his purpose and his own relationship with Toa. Unbeknownst to them, the Lindworm Unit, with the exception of Raina, who is secretly meeting with Garnet, also takes a break at the spa resort. After being spotted, the two groups engage in a battle that breaks the pool's floor, resulting in their separation through underground waterways. Jin and Sieglinde end up with each other, so though some complications arise, past memories allow Sieglinde to soften up to Jin. The two are later found by Gio, who was working with the others in order to find Toa. As both groups reunite, Jin, Toa, and Gio fly off, with Sieglinde allowing them to escape. Meanwhile, back on Earth, Kazuki once again meets the woman, Widow, whom he had met earlier.

After escaping from the spa resort, Jin, Toa, and Gio try to figure out what to do. Jin believes that the three of them can just live peacefully in some small town back on Earth. Despite Toa's desire to do so, she has a "mission" to fulfill, so she abandons Jin and Gio while they are sleep. Once Jin wakes up and realizes that Toa is gone, he tries to look for her, but is thwarted when Kazuki and Widow show up. Kazuki demands Gio back, but Jin is more concerned with looking for Toa. After Gio frees himself from Widow's clutches, he picks up Jin and runs off. Meanwhile, Toa surrenders herself to Raina, who had just been in a meeting with Kō. Still desperate to get Gio back, Kazuki offers to help Jin get Toa back if Jin agrees to give him Gio. His hesitation prompts Kazuki to send Widow to retrieve Toa. When Jin tries to apologize to Gio, Gio asks if Jin can protect Toa, and after hearing that Jin can, Gio realizes that he has been getting between Toa and Jin all along.

It is revealed that when the shuttle exploded two years ago, Sakaki's wife and daughter had been on board. In present time, just when Jin hears Toa tell him that she was responsible for his family's death, the Lindworm Unit suddenly appears to ambush the trio: Jin, Gio, and Toa. Meanwhile, as Garnet and the military look over the Resonance data they received from Raina in exchange for giving up their search for Gio, they realize that it is fake. In retaliation, she later attacks the shuttle carrying the trio. When Gillard Army begin to corner the Dragonauts, they are saved by a fourth dragon from the Vritra Unit, but the Gillard military ships continue their attack. As enemies board the shuttle containing the trio, Gio makes Jin, who has been focused on Toa's confession, remember his promise to protect Toa. Gio then actualizes with Jin as his pilot. They quickly destroy most of the enemy's forces, causing Garnet to retreat.

During an ISDA meeting, Kazuki's actions as a Dragonaut, and the current situations of the Album, Jin, Gio, and Widow are discussed. Meanwhile, Gio and Widow are confined in a facility that prevents them from leaving. At the ISDA base, Yuuri explains the Resonance process to Jin, and tells him that he had resonated with Toa two years ago. Elsewhere, Garnet is trying to apologize for her failures to Prince Asim, but he is now more interested in obtaining Toa rather than Gio. Back at the ISDA, Toa breaks free and attempts to retrieve some dragon eggs, but Kasuga's glowing eyes make her hesitate, giving Amadeus a chance to knock her unconscious. Using the confusion caused by Toa's attempt to escape, Akira and Machina free Jin. Laina and Howlingstar attempt to stop them, but after Machina uses Laina as a hostage, they end up successfully escaping. Later, when the ISDA decide to transport Toa, they are attacked by the Gillard military.