Much to the horror of Meiko Mochizuki, her Digimon partner Meicoomon is forced to evolve into Meicrackmon and falls under an evil influence in the process. As Meicrackmon disappears to wreak havoc elsewhere, it seems that the Digital World itself starts to reject the presence of Meiko and the other Chosen Children. While evading various enemies who come after them, the group attempts to find their way back home. In the human world, a messenger from the mysterious entity Homeostasis visits both Meiko's father and Daigo Nishijima of the Incorporated Administrative Agency to discuss Meicoomon's origins. The messenger informs the two that Homeostasis plans to eliminate the digital monster. By doing so, they hope to prevent further Digimon from materializing in the human realm—regardless of the Chosen Children's feelings on the matter.

A catastrophic earthquake has left Tokyo, and most of the Earth for that matter, under the sea. Aika is a salvager who retrieves various remains from the watery ruins. When Aika accepts the dangerous mission of locating and obtaining the mysterious Lagu, she discovers that she's not the only one after it.

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.

The conclusion of the Mino ware contest has spurred Himeno Toyokawa to create a piece even more remarkable than the last. Anxious to embrace the future yet emboldened by her mother's legacy, Himeno strives to find the right inspiration—a task that proves to be just as ambitious as her goal. When Himeno's father suggests that her next creation should be the centerpiece at the cafe, expectations for the final product only grow with each passing day. Through new encounters and experiences, Himeno and her friends reconnect with the foundation of their passion in their search for what lies at the core of pottery.