An accidentally made time machine is going to start the third world war. But before most people are killed, the two ladies closest to Rintaro might be meeting their deaths. When Rintaro and Mayuri go to a conference, they stumble upon the body of Kurisu. Alarmed, Rintaro sent a mail back to his friend.

However, he has no idea that the mail reached the past, and time is changed. Kurisu is alive in this timeline, and from her, he learned of a group called SERN. SERN will do anything to gain control of the time machine. To thwart them, Rintaro has to travel back time repeatedly and lie to a lot of people.

Because if he doesn't, the girls he's closest to are going to die again, and this time, no time machines are going to help them.