The anime takes place in a world that long ago featured the existence of magic, but has long since lost that ability. The story begins when the very normal high school student Mangetsu Kohinata meets Shingetsu Ernesta Fukami, who has migrated back to Japan from Germany, on a night with a full moon.

X-Men, still grieving over the death of Phoenix (Jean Grey), are investigating a case of a missing mutant girl in Northern Japan. This leads them to a mysterious virus that turns mutants into monsters. U-Men and the Inner Circle want it.

The dark untold story of Steins;Gate that leads with the eccentric mad scientist Okabe, struggling to recover from a failed attempt at rescuing Kurisu. He decides to give up and abandons his lively scientist alter ego, in pursuit to forget the past. When all seems to be normal, he is seemingly pulled back into the past by meeting an acquaintance of Kurisu, who tells him that they have begun testing a device that stores the memory of a human and creates a simulation of them with their characteristics and personalities. Okabe begins testing and finds out that the simulation of Kurisu has brought back anguish and some new unexpected tragedies.

Zero is a side story that explores events from the Beta Attractor Field’s future that contribute in making the end of the original story possible.

A group of friends have customized their microwave so that it can send text messages to the past. As they perform different experiments, an organization named SERN who has been doing their own research on time travel tracks them down and now the characters have to find a way to avoid being captured by them.