The eccentric, self-proclaimed mad scientist Rintarou Okabe has become a shell of his former self. Depressed and traumatized after failing to rescue his friend Makise Kurisu, he has decided to forsake his mad scientist alter ego and live as an ordinary college student. Surrounded by friends who know little of his time travel experiences, Okabe spends his days trying to forget the horrors of his adventures alone.
While working as a receptionist at a college technology forum, Okabe meets the short, spunky Maho Hiyajo, who
later turns out to be the interpreter at the forum's presentation, conducted by Professor Alexis Leskinen. In front of a stunned crowd, Alexis and Maho unveil Amadeus—a revolutionary AI capable of storing a person's memories and creating a perfect simulation of that person complete with their personality and quirks. Meeting with Maho and Alexis after the presentation, Okabe learns that the two were Kurisu's colleagues in university, and that they have simulated her in Amadeus. Hired by Alexis to research the simulation's behavior, Okabe is given the chance to interact with the shadow of a long-lost dear friend. Dangerously tangled in the past, Okabe must face the harsh reality and carefully maneuver around the disastrous consequences that come with disturbing the natural flow of time.
本作的故事发生在游戏发售后一年的2010年,背景为现代日本,舞台从涩谷转移至秋叶原。其世界观與前作CHAOS;HEAD共通,但兩部作品之间並無直接關係。
故事开始于2010年7月28日,“未来道具研究所”社团的两人,冈部伦太郎和椎名真由理去秋叶原广播会馆参加中鉢博士的时间旅行理论发表会,见到了年仅18岁就在《科学》杂志上发表学术论文的天才少女牧瀨紅莉栖。发表会结束不久后,在会馆8楼深处,冈部发现了身上滿是鮮血的紅莉栖。惊慌失措的他带着真由理立刻离开会馆,给社团另一成员橋田至发送一条电子邮件告知这一事件。然而发送后的瞬间,冈部愕然发现街道人群消失,广播会馆及周围早已因不明人造卫星坠落缘故被封锁,没有人记得他所经历的事件。
数小时后,冈部和阿至在大学讲习现场再次遇见紅莉栖,引发一阵骚乱。对冈部所说的话感到兴趣而至“未来道具研究所”的红莉栖偶然见到了冈部他们进行的实验,一连串研究发现冈部发送的电子邮件在一周前被收到!“未来道具研究所”研制的未来道具8号“电话微炉(暂名)”竟然具备着将电子邮件发送到过去这一时间机器的功能。此时,冈部他们还不知道,这一发明,和他那封送到过去的電子郵件,已经影响了整个世界的未来……
作品中從架空的事物到實際存在的企業、大學、商品都以真名登場,現實中流传的都市傳說、陰謀論、網路語言等話題也有提及。故事的核心由自稱為未來人、實際上存在的網路人物约翰·提托所流傳的話語、通过主人公的言行和手機进行操纵的游戏系统、网络上流传的“la jodaso stiana(食堂之男)”等为主题的小故事等构成,并借此虚实结合地展开故事。其开始时稍难理解,过半时突然展开。其中多有伏笔,结尾一气呵成。有评论称本作品“通关后还想消除记忆再来一次”。