Several months after a probe returning from Mars burns up during reentry, strange creatures dubbed Ancients begin to appear throughout Tokyo. Aggressive and dangerous, they cannot be killed with ordinary weapons. As scientists struggle to find the cause of their sudden appearance, the monsters wreak havoc across the world. Humanity finds hope in the form of the MARS suit—a new weapon developed to take down these enemies. The suit, however, can only be worn by those with specific DNA. Enter Takeru Hinata, an ordinary teen with a troubled past and one of the few capable of piloting the only weapon against the Ancients. With the help of the AAST, a special police force established to defeat the dangerous creatures, the young man battles against demons both personal and global whilst trying to discover the true nature of Earth's new aggressors.

Takuma Hirose is a blind young male high school student, though the cause for his blindness is undetermined. In order to heal his medical condition, he is sent to live in a village with his uncle. There, he meets several girls, three of which stand out more than any of the others. They are Hayami Kohinata, Hinata Kangura, and Otoha. Otoha temporarily heals his blindness and Hirose uses his sight to help others. He finds out that, for some reason, Hayami Kohinata is hated in the village, and he tries his best to help her out. Meanwhile, many sad secrets unfold in the village...

As the season changes from spring to summer, Makoto Yuuki remains alongside the Specialized Extracurricular Execution Squad (SEES). The team continues to defeat Shadows large and small, but they now clash with a new enemy: Strega, a group of rogue Persona users who wish to keep the Dark Hour to their advantage—it seems that Strega may hold a clue to the Dark Hour's true nature. While SEES enjoys summer vacation in Yakushima, they are joined by Aegis, an amnesiac android designed to destroy Shadows. While she proves herself to be a powerful ally, she is inexplicably drawn to Makoto and constantly remains at his side. As they delve deeper into the mysteries of the Dark Hour, the nature of the mysterious connection that binds these two together is slowly unveiled.

Noah's Ark—the latest in VR technology and a milestone of human innovation—is set for a showcase to Japan's privileged children. They have the honour of beginning a new revolution in gaming; however, their carefree fun is cut short when a company employee is found murdered, with his dying message pointing to a clue hidden within the Ark. Along with the Detective Boys and Ran Mouri, Conan Edogawa enters Noah's Ark to solve this mystery and ensure the perpetrator is caught. But once they're inside the Ark, it takes on a mind of its own, imprisoning them and the children within its worlds. To escape and bring the murderer to justice, Conan and company must navigate a simulated 19th century London and track down the infamous Jack the Ripper—with the lives of 50 innocent children depending on them.