The film takes place in August 2011, one year after the events of the anime series. After going through a painstaking journey across multiple 'World Lines' due to the invention of 'D-Mail', text messages that can be sent to the past, Rintaro Okabe has assumedly landed in the "Steins Gate" World Line, in which he was able to prevent the deaths of both Mayuri Shiina and Kurisu Makise, as well as prevent a future ruled by SERN due to the invention of a time machine that no longer exists. On August 3, Kurisu arrives in Japan for a press conference and reunites with all the members of the Future Gadget Laboratory. Meanwhile, Rintaro starts having intense side effects from his time travels, seeing visions of alternate Worldlines. The next day on August 4, a mysterious visitor shows up at Kurisu's hotel, telling her to remember three things: a cell phone, a microwave oven, and SERN. Later that day, as Kurisu is talking to Rintaro about how her own instances of déjà vu may be similar to Rintaro's 'Reading Steiner' ability to remember things from other World Lines, Rintaro suddenly disappears before Kurisu's eyes. Furthermore, no one else seems to remember Rintaro ever existed, with Kurisu barely retaining a faint memory of someone.
A week later on August 11, as Kurisu finds a fork that Rintaro left behind and remembers the words the stranger left her, she learns Itaru "Daru" Hashida had for some reason hacked SERN, suddenly giving her the urge to build a Time Leap machine. Using the machine, Kurisu leaps back to the night of August 3, where she observes Rintaro disappearing and reappearing from existence, with everyone's memories of him changing accordingly. She is then contacted by the visitor from before, revealed to be Suzuha Amane, who came from the future using a time machine Kurisu built. She explains to both Kurisu and Rintaro that all the memories of World Lines Rintaro had visited is overloading his Reading Steiner, causing him to fluctuate between the current world line and the "R" world line, the only other world line where neither Mayuri nor Kurisu die. Suzuha states the only way to save him from vanishing completely is to use a time machine to travel to the past, but Rintaro ostensibly refuses, as he feels neither time machines nor time leap machines should exist and doesn't want Kurisu to go through the same suffering he went through, saying he would rather disappear to allow her and Mayuri to live in peace. He instead urges Kurisu to forget about him, leaving her with a kiss.
As Rintaro disappears once again the next day, Kurisu breaks down in tears before grudgingly deciding to accept his wish and try to forget him. Later, on August 13, as the Future Gadget Lab gets word that it might have to close up, Kurisu is once again approached by Suzuha, who tells her that she is not being honest with her own feelings, eventually convincing Kurisu to go with her in her time machine. In order to keep Rintaro in the Steins Gate world line, he must be implanted with a powerful memory that helps distinguish it from other world lines. The two travel back to June 30, 2005, where Kurisu attempts to talk with the young Rintaro, only to result in him getting into a car accident instead, leaving her too afraid to attempt another trip to the past. Back in the present, Kurisu discovers Mayuri and the others also possess faint memories of Rintaro, which are soon awakened when she does an imitation of his persona, Kyouma Hououin. Encouraged by everyone's feelings, Kurisu returns to the past, this time succeeding in her mission by implanting the concept of Kyouma Hououin into Rintaro's mind and giving him his first kiss, which led him to take on his 'mad scientist' persona to protect Mayuri. With this, Kurisu manages to bring Rintaro back to the Steins Gate world line and the movie ends with Rintaro asking Kurisu if she will return his first kiss to him. Smiling, Kurisu says "Never".