present day
Twenty years after the presence of Thanatos was first detected and two years after the shuttle accident that claimed forty-eight lives, things return to something of an established norm within the ISDA. After Nozaki Kasuga's presence accelerates dragon research, a fully-established Dragonaut team ("The Lindworm Unit") is created. This group of masters and dragons are designated to fight against Thanatos should the need arise.
An eighteen-year-old Kamishina Jin continues studying, oblivious to the truth about the ISDA shuttle crash, until his life is inadvertently threatened by one of the Lindworm Unit's dragons. It is then that he is reunited with Album (now going by the name "Toa"), the dragon that had Resonated with him during the shuttle disaster. During the subsequent battle with the berserk dragon, Toa's calls foster the premature birth of a dragon egg that had Resonated with Jin's former best friend, Tachibana Kazuki. The newly born dragon (known a "Gio") feels compelled to protect Toa over any will of his own master.
Alerted to the presence of an "original" dragon, the ISDA decides to capture Toa. At first Kitajima refuses to get her hopes up when presented with a photograph of Toa by her ex-lover (Yonamine) but she eventually comes to the conclusion that Album has truly returned and thus begins her infatuation with the dragon's capture.
Over the course of twelve episodes, the Dragonauts waver between helping Toa + Jin and attempting to capture them. Along the way the leads discover Toa's role in the demise of the ISDA flight two years previous and Jin's apparent Resonance with her. Things come to a head when Toa is captured by the ISDA and primed for Kitajima's tests only to have Nozaki cease the experiments. Nanami then convinces Kitajima to take the dragon to Tartarus (a dragon holding compound) only to betray her senior by handing Toa to her true comrades in the Gillard Army (from the New Gillard Emirates whose leader, Prince Asim, resides on Mars).
With Toa in Asim's custody on Mars, she is unable to contact Thanatos. After Toa ceases contact with her, Thanatos decides to cut her losses and wipe out her remaining children along with Earth. Thanatos sends a dragon dubbed "Ostrum" to destroy the planet and the unhatched dragon eggs held deep within the ISDA. After her unsuccessful attempt to hold Toa on Tartarus, Kitajima returns to the ISDA only to witness Nozaki destroying Ravum's body — the one remaining link to the original dragons. Just as she begins to break down over the loss of all her research material, Ostrum appears in the facility and Nozaki is forced to reveal his true form — that of the lost original dragon, Atrum.
The Dragonauts (with Jin and Gio's help) manage to blow Ostrum up outside Earth's atmosphere, saving the planet (albeit briefly). The main ISDA base leaves for the Moon with Kitajima and Nozaki opting to stay on Earth to protect the dragon eggs. Gio and Jin rush to Mars in order to save Toa from Asim. While on the planet their companions, Akira and Machina, die trying to protect the dream of peaceful dragon and human interaction. Asim reveals that his trusted general Garnet is actually a dragon and the pair die in battle against Gio. Toa and Jin escape harm but Gio goes berserk and sets Mars ablaze. The three eventually return to Earth — safe, but now estranged from the ISDA and the Dragonauts that had supported them.