One year after the events of the anime, Rintarou begins to feel the repercussions of extensive time travel, and eventually completely fades from reality. Kurisu, being the only companion to remember him, now must find a way to bring him back.

History is coming to an end. When humans came down from the sky they brought with them the Testament, the guide to the path they must follow if they wish to return to the skies again.

When a certain man is released from prison, he knows exactly where he's heading first. After falling in love with a traditional comic storyteller's rendition of the story called "Shinigami," he is determined to become his apprentice. The performer, Yakumo, has never taken an apprentice before, but to everyone's surprise, he accepts the eager ex-prisoner, nicknaming him "Yotaro." As Yotaro happily begins his new life, he meets others in Yakumo's life, including Yakumo's ward Konatsu. Konatsu was the daughter of a famous storyteller, and Yakumo took her in after her father's tragic death. Konatsu loved her father's storytelling, and would love to become a performer in her own right—but that path is not available for women.

A teacher takes all aspects of life, word and culture in the most negative light possible.

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.

During the early 1930s in Chicago, the transcontinental train, Flying Pussyfoot, is starting its legendary journey that will leave a trail of blood all over the country. At the same time in New York, the ambitious scientist Szilard and his unwilling aide Ennis are looking for missing bottles of the immortality elixir. In addition, a war between the mafia groups is getting worse. On board the Advena Avis, in 1711, alchemists are about to learn the price of immortality. Takes place in the same universe as Durarara (2010).