After a year in America, Kurisu Makise returns to Akihabara and reunites with Rintarou Okabe. However, their reunion is cut short when Okabe begins to experience recurring flashes of other timelines as the consequences of his time traveling start to manifest. These side effects eventually culminate in Okabe suddenly vanishing from the world, and only the startled Kurisu has any memory of his existence. In the midst of despair, Kurisu is faced with a truly arduous choice that will test both her duty as a scientist and her loyalty as a friend: follow Okabe's advice and stay away from traveling through time to avoid the potential consequences it may have on the world lines, or ignore it to rescue the person that she cherishes most. Regardless of her decision, the path she chooses is one that will affect the past, the present, and the future. [Written by MAL Rewrite]

Deep in the Ararat Mountains of Turkey, a secret organization known as ARCAM has found what is believed to be Noah's Ark. However, the U.S. Machine Corps., a rogue organization of the Pentagon, wants to take over the Ark as a means of global supremacy. Only a special ARCAM operative known as a Spriggan stands in their way. Japanese Spriggan Yu Ominae teams up with French Spriggan Jean-Jacques Mondo to combat members of the U.S. Machine Corps. led by Col. MacDougall—a genetically-enhanced boy with deadly psionic powers. However, they must act fast and stop MacDougall before he uses the Ark for his own agenda. (Source: ANN)

In the story, the seasons have changed and it will soon be the second spring. Tatsuya and Miyuki have finished their first year at First Magic High School and are on their spring break. The two go to their villa on the Ogasawara Island archipelago. After only a small moment of peace a lone young woman named Kokoa appears before them. She has abandoned the Naval base and she tells Tatsuya her one wish.

(Source: ANN)

In the Japan of the future, employing androids for various purposes is nothing out of the ordinary. However, treating androids on the same level as humans is frowned upon, and there is constant paranoia surrounding the possibility of robots defying humans, their masters. Those who appear too trustworthy of their androids are chided and labeled "dori-kei," or "android-holics."

High school student Rikuo Sakisaka notices when his house droid, Sammy, starts behaving curiously—she has been leaving the house without his instruction. When he inspects the movement logs in her database, a cryptic line grabs his attention: "Are you enjoying the time of EVE?" Accompanied by his friend Masakazu Masaki, Rikuo tracks the whereabouts of his houseroid to a cafe called Time of Eve, where it is forbidden for customers to display prejudice against one another. The cafe, Rikuo realizes, is frequented by both man and machine, with no evidence to tell either apart.

Each customer—from the cheerful Akiko, to a robot dangerously close to breaking down—has their own story and challenges to overcome. While Rikuo tries to reveal Sammy's intentions, he begins to question the legitimacy of the fear that drives humans to regard androids as nothing more than mere tools.

[Written by MAL Rewrite]