Years after a young boy in America loses one of his Digimon friends, an evil viral Digimon successfully kidnaps the original Chosen Children. Their younger friends must race against time with their Digimon partners to discover the source of this new menace, and perhaps solve a years-old mystery.

(Source: ANN)

Mikiya Kokutou gives Shiki Ryougi a cat to watch, as he will be away for a little while. Though Shiki protests, he leaves the cat anyway, and Shiki is stuck trying to understand her new feline companion. But as luck would have it, the cat seems to have taken a liking to Mikiya and misses him.

Later in another part of the city, Ririsu Miyazuki visits the place where her dear friend committed suicide. She intends to end her life as well, but she meets Fujino Asagami, a blind classmate with a traumatic past. Though the two girls don't have much in common, Asagami reminds Miyazuki of her lost friend and helps her understand her pain.

Two months later, Mikiya elects to celebrate New Year's with Shiki instead of his family, which makes his sister Azaka very upset, leading to her spending the holiday with her school friends. As the snow begins to fall, Mikiya reflects on what he wishes for most of all: that Shiki's life be filled with happiness.

[Written by MAL Rewrite]

A young girl named Zuru sets out on an expedition through a post-apocalyptic city controlled by machines in a desperate hunt for food. Things go awry when her team accidently triggers the city's AI defense program called the Safeguard. Attacked by the machines, her companions are on the verge of being annihilated when a mysterious man named Killy arrives and exterminates the hostile units.

Despite his heroic intervention, Zuru is hesitant to trust Killy and questions his motives. He reveals to have come from thousands of levels below the city in order to find humans possessing the Net Terminal Genes—a trait that would allow humans to regain control of their civilization and shut down the Safeguard. After hearing his story, Zuru and the rest of her team join Killy and embark on a journey in search of the Genes that could prove to be mankind's last hope of survival.

[Written by MAL Rewrite]

Take place 2 years after the last episode of the TV series.

Detective Sonia Summers are tracking Bem and the others. She reunited with Belo, who is fighting a dark organization alone. He brought her to Bem, but Bem doesn't remember anything and living in the city as an ordinary employee... or that is what he thought he was.