舞台は2010年夏の秋葉原。厨二病から抜け出せない大学生である岡部倫太郎は、「未来ガジェット研究所」を立ち上げ、用途不明の発明品を日々生み出していた。 だが、ある日、偶然にも過去へとメールが送れる「タイムマシン」を作り出す。 世紀の発明と興奮を抑えきれずに、興味本位で過去への干渉を繰り返す。 その結果、世界を巻き込む大きな悲劇が、岡部たちに訪れることになるのだが… 悲劇を回避するために、岡部の孤独な戦いが始まる。果たして彼は、運命を乗り越えることができるのか！？
Though WWIII is on the horizon, Okabe attempts to live a normal college life. However, a newly developed AI is about to shake up his world.
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 Okabe Rintarou briefly has a vision of a world line where he is caught up in the middle of a war, which he eventually comes to realize 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-traveled with her from the year 2036 but became separated from her in 1998. As Rintarou 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.
The armed men attempt to abduct Kagari but are forced to flee empty-handed when Yugo Tennouji arrives and disarms them. Concluding that group are not the same Rounders he had previously encountered, Rintaro approaches Tennouji, using his knowledge over him being a member of a Rounders to acquire his help in protecting Kagari. Meanwhile, as Maho continues to find herself locked out of Amadeus, Ruka tries to question of Suzuha over what everyone is keeping from him. Later, Rintaro suddenly receives a distress call from Amadeus, at which point his Reading Steiner activates and he is sent to another world line where Kurisu is still alive.
Rintaro soon comes to realise that he has once again ended up in the alpha world line where Mayuri is dead, as the Rintaro of this world line couldn't go through with sacrificing Kurisu in order to save her. Realising that this Rintaro came from another world line, Kurisu reveals she has rebuilt the Phone Microwave, asking him to use it to return to his world line. As Rintaro struggles with his decision, Kurisu takes him to Mayuri's grave, urging him to wake up from his dream. After advising Rintaro not to interact so much with Amadeus, Kurisu kisses Rintaro before sending a D-Mail, returning him to the beta world line.
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.