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 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.

The episode was rated 8.03 from 269 votes.

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.

The episode was rated 8.05 from 263 votes.

As Kurisu offers to look after Mayuri at a doujin convention, Rintarō heads to Moeka's address, only to learn that she had killed herself. After finding out the deadline of Mayuri's death in this world line, Rintarō time leaps to before Moeka killed herself, finding her in a nervous wreck having not been contacted by someone known as 'FB'. Rintarō steals Moeka's phone and sends a D-Mail from it, but the timeline doesn't shift, leading him to realise that another message was sent from her phone. Rintarō confronts Moeka about FB and tells her about her future suicide. Rintarō finds the offending mail, which involved the location of the IBN-5100, but sending a D-Mail from that phone doesn't affect the world line. As Rintarō decides he needs to send a D-Mail from FB's phone, Moeka tells him the location of the IBN-5100.

The episode was rated 8.06 from 241 votes.

Not wanting to move to a World Line where Kurisu dies, Rintarō decides against the hacking. As he accompanies Mayuri to a Comic Market, he tries to think of a way he can save her without changing World Lines, too afraid to tell Kurisu the reason behind his change of plans. As a car appears during Mayuri's fated time to die, Rintarō attempts to change her destiny by letting the car hit him instead, but Mayuri ends up dying trying to save him. After he leaps back in time, Kurisu has Rintarō reveal to her that she dies in the Beta World Line. As Rintarō finds Mayuri visiting her grandmother's grave, he overhears that she's been having dreams of the times she has died, and about how she has noticed Rintarō's suffering.

The episode was rated 8.09 from 246 votes.

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.

The episode was rated 8.10 from 273 votes.

Despite the change in divergence, Mayuri's death still takes place, albeit a day later than in previous timelines. Rintarō asks for Kurisu's help, who theorises that, since negating Rintarō's D-Mail about Suzuha delayed the attack, undoing the effects of the other D-Mails could bring them back to a World Line where they have an IBN-5100, letting them hack into SERN and delete the records that set them on Rintarō's trail. Rintarō starts by trying to figure out how to reverse Rumiho's D-Mail, while helping her evade a rival gaming gang. Rintarō takes Rumiho to the place where her maid cafe used to be and tells her about the way Akihabara was. Rumiho comes to remember the previous timeline and the D-Mail she sent: a fake ransom note, which prevented her father from boarding a plane fated to crash. The rival gang catches up to them but they are rescued by the arrival of Rumiho's father. Speaking to him, Rintarō learns that Suzuha gave him the IBN-5100, but he was forced to sell it in order to pay for the fake kidnapping's ransom. After accepting the reality of her father's death, Rumiho agrees to send a D-Mail cancelling out her previous one, turning Akihabara back into a moe hub. The IBN-5100, however, still remains out of reach.

The episode was rated 8.18 from 249 votes.

Despite Rintarō knowing the location of the IBN-5100, Kurisu is against him trying to steal it, as it most likely won't affect the world line. Instead, she suggests to Rintarō that he stake out the location in order to find FB, with Moeka deciding to join him. As they observe the IBN-5100 being taking out, they follow it as it is passed along to several people, including Mr. Braun, before it ends up on a plane towards France. Rintarō, Moeka and Kurisu go to confront Mr. Braun, who reveals himself to be FB, killing Moeka before taking his own life. Rintarō uses Braun's cell phone to cancel out Moeka's D-Mail, returning to a World Line where both Moeka and Braun are alive and he possesses the IBN-5100. As Rintarō gets Hashida to hack into the SERN network to erase the data they have on them, he comes to sudden realisation that he needs to undo an additional D-Mail: the one that prevented Kurisu from getting stabbed.

The episode was rated 8.36 from 256 votes.

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.

The episode was rated 8.46 from 275 votes.

Unable to get much information about the badge maker's client, Rintarō decides to leap back in time to confront the client in question, only to find it was Hashida, who wanted to make a fake badge to cheer Suzuha up. Hashida then mentions that Suzuha's time machine is only able to travel backwards in time. As the repairs to the time machine are completed, Mayuri deduces from the time machine's naming convention that Suzuha's father is actually Hashida. After a short reunion, Suzuha travels back to 1975, though Rintarō notices the Divergence Meter's reading hasn't changed. Later, Mr. Braun delivers a letter from Suzuha from the year 2000, mentioning that she commited suicide a year later. In the letter, Suzuha laments that she failed her mission, as the damaged time machine caused her to lose her memories for 24 years. Rintarō blames himself for stopping her on the night of the party and, despite Mayuri's pleas, sends a D-Mail that stops him from following Suzuha, letting her use the time machine before it was damaged. Speaking with Mr. Braun again, Rintarō learns that Suzuha has died of illness instead, leaving behind her Divergence Meter. Noticing a small change in divergence, Rintarō returns home and finds Mayuri has not been killed by Moeka.

The episode was rated 8.55 from 264 votes.

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.

The episode was rated 8.57 from 280 votes.

Suzuha explains that her mission is to prevent Kurisu's death and enter a World Line known as 'Stein's Gate' so that World War III will never happen. With a small chance of saving Kurisu, Rintaro agrees to go with Suzuha to just before Kurisu's death. As Rintaro waits in the place where Kurisu's stabbing takes place, he sees Kurisu's father, the Professor Nakamachi he saw that day, attack Kurisu as he tries to steal her time travel theory. As Rintaro attempts to save Kurisu, he inadvertently stabs her himself, allowing Nakamachi to escape with her theory and bring it to Russia. Returning to the present, Rintaro falls into despair but Mayuri knocks some sense into him. Afterwards, Rintaro receives a video mail from his future self, telling him that the key to saving Kurisu without changing the events that led him to create a time machine is to fool his other self into believing Kurisu had died.

The episode was rated 8.58 from 265 votes.

As Rintarō and Kurisu hide out from the rain, she explains how she recalls her stabbing from dreams, as well as Rintarō's various attempts at saving Mayuri. When Kurisu tells Rintarō that he should save Mayuri over her, he can't accept it and runs off. As Rintarō attempts to time leap again, Kurisu stops him, worried that seeing Mayuri die over and over will destroy him. After giving in and choosing to go save Mayuri, Rintarō tells Kurisu he loves her, to which she responds by kissing him. The next day, Kurisu leaves for Japan, whilst Rintarō and the others delete their data from the SERN network. Just then, Kurisu returns to tell Rintarō she loves him, just before the data deletion takes him to the Beta World Line. After getting rid of the Mobile Microwave, Rintarō receives a call from Suzuha, telling him about World War III.

The episode was rated 8.66 from 275 votes.

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.

The episode was rated 8.67 from 267 votes.

Picking up a sabre toy in order to use its liquid as a substitute for Kurisu's blood, Rintaro and Suzuha return to the day of Kurisu's death. First, he makes sure to obtain a metal toy Mayuri previously found in order to prevent Nakabachi to successfully bring Kurisu's theory to Russia. As he prepares to fake Kurisu's death, Rintaro finds the liquid in the sabre had dried up. To this end, he allows himself to be stabbed by Nakabachi, before knocking out Kurisu with a taser and using his own blood to set the scene up for his past self. As Rintaro returns to the past, Suzuha gives her thanks before time is altered so that the time machine was never invented. In this new timeline, Rintaro goes around giving badges to his past lab members, eventually managing to meet Kurisu once again; she was looking for Rintaro to thank him for saving her life, suggesting that the event of their romance doesn't disappear, either.

The episode was rated 9.09 from 282 votes.