Six months have passed since Rintaro Okabe, unable to change the past, chose to stay in a world line where Kurisu Makise is dead, discarding his identity as a self-proclaimed mad scientist. Suzuha Amane, the future daughter of Itaru Daru Hashida who had traveled back in time to convince Rintaro to help her prevent World War III, has been pretending to be Daru's sister to keep her identity a secret from her future mother, Yuki Amane. As Rintaro, still traumatized over his experiences with changing world lines, continues to refuse to help Suzuha, he attends a seminar held by Professor Alexis Leskinen and his assistant Maho Hiyajo. Prior to the seminar he became shocked to find Moeka Kiryu with them. During the seminar, Leskinen and Maho present Amadeus, an artificial intelligence program based on Kurisu's research before her death.

After a chance encounter with Maho where they discover knowing someone in common, Okabe has his first face-to-face with her special AI, Amadeus.

Mayuri tries to bring everyone together for a Christmas party at the lab, but Okabe has a rude awakening.

While OkaRintaro briefly has a vision of a world line where he is caught up in the middle of a war, which he eventually comes to realise was his Reading Steiner taking effect. Meanwhile, Suzuha explains to Daru that she is looking for Kagari Shiina, Mayuri's future adopted daughter who time-travelled with her from the year 2036 but became seperated from her in 1998. As Rintaro decides to help with the search, he gets a call from Ruka Urashibara about a pressing matter before finding Moeka before his doorstep. be is left with more questions than answers, Suzuha recruits help in her search for an unexpectedly close person.

Their search continues as New Years swiftly approaches, though Ruka's dilemma with a certain guest might make matters worse.

Now that the girl's identity is known, Okabe and friends kick off the New Years with a shrine visit and party to never forget.

As Okabe seeks answers regarding the attack, trouble with Amadeus brings a surprising turn of events.

Okabe is given a bittersweet reminder that in changing world lines, sacrifices must be made.

It will take time for Okabe to identify the attackers and their motivation, but the impending crisis of WWIII forces Suzuha to resort to desperate measures.

After reinforcements are called to clean Maho's disastrous room, her and Okabe's Akihabara date ends with a surprising confession from Maho.

Okabe must convince Maho to give up her prized possession, but an unexpected danger has them negotiating for their own lives.

Kagari attempts to track down the origins of a song in hopes that she discovers her lost memories.

After finally obtaining a hint into Kagari's lost past, Okabe ends up discovering much more than he bargained for.

Shocked by a surprise attack, Suzuha and Daru look to America as their last hope to save the world.

Fed up with her Dad's passiveness, Suzuha must make a man out of Daru before Yuki ends up with somebody else.

Okabe's stubbornness causes fists to fly and tears to be shed as the deadline for using the time machine swiftly approaches.

As Suzuha sets off to finish her mission, Mayuri finds determination of her own. But then, disaster strikes.

All hell breaks loose over the time machine when a villain from the future haunts the past and unveils their devious plan.

War and disaster has come, and the only way Okabe can stop it is to rely on his friends, determination, and hope.

Okabe awakes in a cold, lifeless world where he finds his friends struggling to survive amidst all the chaos.

Okabe is forced to time leap thousands of times in order to continue his plans. Will he finally be able to save his friends?