Immortality is something many people would wish for. But would it be such a coveted ability if people knew they would be subject to countless attacks because of it? Such is the case for Rin Asougi, an immortal private investigator, because there is no shortage of people who want her dead. Over the centuries, she has met many grisly ends, but each time, she returns to life as if nothing had happened. In 1990, while looking for a lost cat, Rin runs into Kouki Maeno, a man who feels that his memories are wrong. Agreeing to help him, Rin discovers that Kouki is not what he seems, all the while drawing closer to her true enemy. This adversary knows Rin and her kind all too well, and if she dies by his hand, she may stay dead permanently.

Said to be humanity's natural enemy, formidable dragons that belong to an ancient bloodline roam the world. Only two ways prove effective to kill a dragon: freezing their blood with silverine—an aura that comes from silver weapons—or letting their bodies be incinerated by sunlight. Young hunter prodigy Leonica is accompanied by her close friend Ragna, who appears to lack the skills necessary in their profession. Moreover, many shun Ragna, considering him cursed because dragons always seem to attack him and slaughter his close ones. Nevertheless, Leonica sees potential in Ragna and gladly partners up with him. Likewise, Ragna feels certain that Leonica is immune to his misfortune thanks to her incredible strength. His confidence is shaken, however, when Ragna dreams of Leonica's death, believing this to be a prophecy. As the destined day arrives, he comes face-to-face with his future self, who bestows him enormous power and memories from the future to ensure Leonica's safety. In order to succeed, Ragna must join forces with a mysterious figure known as Crimson and eradicate all dragons for good.

In the year Cosmic Era 0071, a wartime brawl between two mobile suits results in the destruction of a neutral country. Shinn Asuka finds his entire family killed as casualties of the violence, and swears his life toward a vengeful pursuit of the Earth's Natural forces, under the impression they were the ones responsible for his family's death. Shinn works his way up through the ZAFT military forces, eventually gaining access to the cockpit of the prototype Impulse mobile suit. Athrun Zala, a veteran of the recent war employed in the service of diplomat Cagalli Yula Athha, finds himself drawn into a new conflict between the Naturals and the Coordinators: human beings artificially enhanced before birth and hated by the Naturals for their biological advantages. As the new war rears its head and violence becomes inevitable, Athrun finds himself as a mentor to the bitter Shinn. Athrun must steer the young pilot towards a mindset of mercy before his rage and desire for vengeance consumes him.

After surviving a brutal terrorist attack on Plant Quetta, Suletta Mercury returns to dueling at the Asticassia School of Technology, while Miorine Rembran sits at her injured father's side, waiting to see if he will recover. As the residents of Earth House are preoccupied with their respective troubles, two members of Dawn of Fold—the perpetrators of the attack—secretly infiltrate the school, putting Suletta and her friends at risk. At the same time, Prospera, Suletta's mother, approaches Miorine to propose the continuation of Quiet Zero—a project headed by Miorine's father that can allegedly end all war. Prospera seems to be another political figure with hidden, opposing motives, and whether she truly has Suletta's well-being at heart remains to be seen.