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Rose Tyler meets a mysterious stranger called the Doctor, and realises Earth is in danger.

Suzuha explains how SERN was able to build a time machine and use it to rule the world in 2036. She explains she plans to travel to 1975 to acquire an IBN-5100, but soon discovers her time machine has broken down as a result of the storm on the night Rintarō stopped her from leaving. Rintarō leaps two days before the completion of the time leap machine in order to get Hashida to help fix Suzuha's time machine, whilst Mayuri suggests they also help find Suzuha's father, using his badge as a clue. Suzuha gives Rintarō her Divergence Meter, which keeps track of the magnitude of differences between timelines, and tells him about how he founded the resistance against SERN in the future. After spending the day searching for Suzuha's father, Suzuha gives her thanks to Rintarō before he receives a lead on Suzuha's father from a badge maker.

Rintarō makes several time leaps, but no matter what, Mayuri always ends up dying in some way. In one of those leaps, Rintarō calls out Moeka and holds her at gunpoint, making her reveal that SERN have targeted the lab due to the creation of the time machine and their plan to publicly announce it. As Rintarō falls further into despair, Kurisu gets him to reveal what he knows and offers to help him try to save Mayuri. She sends Rintarō to just before she completed the time leap machine, where he tells her past self what he knows. As they discuss what the cause of Mayuri's death could be, they are greeted by Suzuha, who tells them that in order to save Mayuri, they need to find a specific World Line. She takes them to the crashed satellite, which turns out to be her time machine, and reveals she is "John Titor" and has come from the year 2036.

Right after Moeka kills Mayuri, Suzuha rushes in the lab and creates a distraction, allowing Kurisu to use the time leap machine to send Rintarō back in time to 5 p.m. of the same day. Rintarō drives everyone away from the lab, but wastes most of his time searching for Mayuri. By the time they try to escape the area, the bomb threat has stopped the subway and Mayuri is killed when Moeka runs her over with a car. Rintarō manages to escape the clutches of SERN and leaps to the past again. Using his knowledge of Mayuri's movements from his previous leap, he manages to find her sooner and they visit a different subway station. However, Mayuri dies again when Mr Braun's daughter, Nae, accidentally pushes her in the way of an oncoming train. Devastated, Rintarō vows to keep leaping to the past until he manages to save Mayuri.

With the ability to utilise the LHC, Kurisu completes her 'time leap machine'. However, Rintarō, still tortured by the texts he has received, decides against performing an experiment, instead suggesting they announce it to the public. As the lab members decide to have a party, Kurisu comes into conflict with Suzuha, who claims she is destined to become a SERN spy, but Mayuri manages to calm things down. As a bomb threat is televised, Suzuha, after hearing about the lab's connection to SERN, suspects something is terribly wrong and leaves. Just then, the lab is attacked by a group of armed men, led by Moeka who reveals herself to be from SERN. Demanding Rintarō, Kurisu and Hashida hand over the time machine and come with her, she decides Mayuri isn't needed and kills her.

Rintarō discovers that a television in the electronics shop below the lab is the key to the time slot in which D-Mails can be sent. Kurisu then theorises that it might be possible to send memories back in time in the same manner as D-Mails, effectively allowing people to 'leap' to the past. As Rintarō goes into town with Mayuri to look for parts Kurisu needs, running into Moeka along the way, Suzuha tells Rintarō that Kurisu works for SERN, though Kurisu denies this when asked. Kurisu tells Rintarō about the troubles she has with her father, who grew to hate her when she surpassed him in scientific prowess, though cheers up when Rintarō offers to help them reunite. As Mayuri and Kurisu decide to have a sleepover at the lab, Rintarō receives another sinister text message warning him that he knows too much, later learning that the lab is connected to the SERN network without the lab members' knowing.

Rintarō realises the D-Mail Rumiho sent prevented moe culture from being introduced into Akihabara. As Rintarō wonders why the relationships between his friends hasn't been affected, he comes to realise that Ruka's gender had in fact been changed. Afterwards, Rintarō talks with Suzuha, who revealed she came to Tokyo to try and find her estranged father, mentioning she will leave if she is unable to find him the next day. As Rintarō contemplates holding a party for her, offering the chance to send a D-Mail if she fails, he receives a text message letting him know that someone is watching him. Mayuri mentions how Rintarō fell sick when he was younger, which he believes to be the origins of his 'Reading Steiner', his ability to travel between world lines with his memories intact. That night, after some mishaps in preparing the party, Suzuha doesn't show and simply sends a farewell text to Rintarō. He decides to send a D-Mail to himself telling him to follow her, changing history so she ended up attending the party and staying in Tokyo. In this new timeline, the satellite that had crashed into a building in Akihabara has mysteriously disappeared.

Maid café waitress Rumiho Akiha, a.k.a. Feyris Nyan Nyan, learns about the Mobile Microwave as Rintarō discusses it with Hashida, becoming very interested in it. Later, Rintarō discovers that the IBN-5100 has gone missing, as if they never found it in the first place, most likely as a result of Moeka's D-Mail. After learning that the IBN-5100 had been previously taken from Ruka's shrine, Rintarō finds Moeka in town, but she doesn't know where the IBN-5100 is either. Rintarō also finds out that Ruka's D-Mail has caused Mayuri to know Moeka in this timeline. Rintarō, Hashida and Mayuri go to see Rumiho, whose family owns Akihabara and originally donated the IBN-5100 to the shrine. She offers them a replacement in exchange for being allowed to send a D-Mail ten years into the past. As history is changed again, the IBN-5100 was never donated to the shrine and, more disturbingly, the face of Akihabara has completely changed, no longer being a mecca for anime.

As Rintarō decides to resume his experiments, Moeka requests to send a D-Mail. As she sends the D-Mail, Rintarō is shifted onto a new timeline where Moeka never came to the lab. The next day, Ruka comes to the lab, asking to send a D-Mail to the past so that he would be born as a girl. They send a D-Mail to Ruka's mother's pager from before he was born, letting her know of an urban legend about how mothers-to-be can affect their baby's gender by eating certain foods. Rintarō moves to a new world line, though he doesn't notice anything particularly different at first.

After some improvements are made to the Mobile Microwave, Rintarō decides to experiment changing the past by sending winning lottery numbers to the past. After sending the text, the past is changed to where Ruka has bought a lottery ticket, but Rintarō didn't perform the experiment, with only Rintarō retaining the memory of what had happened, realising time has been put onto a new timeline. Confused as to why only he can remember the previous timeline, Rintarō contacts John Titor, who tells him he may have the power to become a messiah and change the future.