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 episode was rated 8.00 from 270 votes.

Rintarō tells Ruka about how she used to be a man and urges her to reverse the D-Mail responsible in order to change Mayuri's fate. While she initially disbelieves him, ultimately she agrees, on the condition that Rintarō takes her on a date. Despite Kurisu and Hashida's advice on dating, Rukako and Rintarō spend the evening in awkward conversation. Like Rumiho, Ruka eventually recalls the previous timeline, which makes her even more depressed at the impending return to it, since she feels she will be unable to pursue her feelings about Rintarō as a guy. Before sending the D-Mail that will cancel out Ruka's first one, Rintarō realises that the reason she didn't enjoy their date was that he was trying to be someone he's not. He visits the shrine and tells her that, no matter what, she'll always be his "student". With their relationship repaired, the world line shifts, turning Ruka back into a guy and leaving only one more D-Mail to be reversed: Moeka's.

The episode was rated 8.00 from 245 votes.

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.

The episode was rated 7.94 from 266 votes.

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.

The episode was rated 7.90 from 303 votes.

Okabe is shocked to learn that Akihabara is now devoid of moe culture. He questions Mayuri and Daru about Toranoana and other stores that used to be the city, but Mayuri insists that they never existed in Akiha to begin with. Okabe finds that even May Queen Nyan-Nyan has been replaced. He is awe by just how much one text message changed their world.

The episode was rated 7.76 from 266 votes.

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.

The episode was rated 7.70 from 325 votes.

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.

The episode was rated 7.65 from 283 votes.

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.

The episode was rated 7.58 from 345 votes.

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.

The episode was rated 7.55 from 319 votes.

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.

The episode was rated 7.31 from 452 votes.