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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.

The lab members discuss how to perfect the Mobile Microwave, dubbing messages sent to the past as 'D-Mails'. Further experimenting reveals the various rules concerning D-Mails; being that it can only be sent during a certain time of the day, long messages are split into several smaller mails, and the timer on the microwave determines how far back the message is sent. The next day, Moeka comes round to see the IBN 5100 and, after hearing about the time experiments, is made a lab member.

As Rintarō and Kurisu arrive home with the IBN 5100, Suzuha seems to be shocked when she sees Kurisu. As Rintarō gathers some needed parts, he runs into Suzuha again, who warns her to be cautious of Kurisu and acts strangely when a helicopter passes by. After Hashida gets the IBN 5100 working, he, Rintarō and Kurisu begin deciphering SERN's reports. They discover that they had indeed been experimenting with time travel, with their attempts of sending humans back in time resulting in the same jellification Rintarō had performed on the bananas. With this knowledge, Rintarō becomes determined to perfect his Mobile Microwave.

With further information encrypted in a code that Hashida can't decifer, Rintarō learns from John Titor that he needs the IBN 5100 computer Moeka was looking for to decode it. Whilst doing his laundry, Rintarō runs into Kurisu, who is still in denial about a time machine existing. After Mayuri hears from her co-worker, Feiris Nyannyan, that she knows about the IBN-5100, Rintarō plays a game before learning that the computer is at the shrine where Ruka works. After getting permission to borrow it from Ruka's father, Rintarō and Kurisu carry it back to the lab.

Rintarō agrees to let Kurisu look at the mobile microwave on the condition she become a lab member. They discover that Hashida was using the microwave at the time Rintarō sent his text about Kurisu's stabbing. Despite the microwave causing a large electrical discharge when Mayuri opens it in the middle of operating, Rintarō concludes that the mobile microwave is, in fact, a time machine. After hearing about the large hadron collider and micro-black-holes, Rintarō asks Hashida to hack into CERN's network. There, they discover they had already been performing micro-black-hole experiments, kept hidden from the public, which reveals that humans had died during them.

Rintarō is surprised that Kurisu is alive, before being humiliated by her during a lecture concerning time travel. After getting some provisions from crossdresser Ruka Urushibara and meeting Suzuha Amane, who gets hired to work part time in the electronic's shop below his apartment, Rintarō investigates the supposedly altered events and learns of a man calling himself John Titor who claims to be a time traveller. Rintarō then discovers the books he had on John Titor had disappeared as if they never existed. The next day, Rintarō encounters a strange woman named Moeka Kiryū who asks for information on a retro PC, which Rintarō gathers from Hashida. Later, whilst testing a banana on their microwave which then disappears, Rintarō and Hashida find the banana reattached to the bunch it came from in its gelled state, before Kurisu appears before them once again.

Self-proclaimed mad scientist, Rintarō Okabe, goes to a seminar on time travel with his friend, Mayuri Shiina. Whilst there, he meets a girl named Kurisu Makise who explicitly states that he had met her 15 minutes ago, despite having never met her before. Later on, Rintarō hears a scream and discovers Kurisu had been stabbed. As he sends a text to another one of his research buddies, Hashida Itaru, Rintarō experiences a strange experience and finds the street he is on has suddenly become deserted and a strange sattelite had crashed into the building he was just in. Later on, whilst fiddling about with their strange remote-controlled microwave, which turns bananas into a gel-like substance, Hashida tells Rintarō that the seminar he supposedly attended was cancelled, much to his surprise. Rintarō later discovers that the text he sent to Hashida had been sent to a week ago, just before encountering Kurisu, who is alive and well.