Time Travel Shoujo is based on a 1983 book titled Jishaku to Denki no Hatsumei Hakken Monogatari by Japanese educator Kiyonobu Itakura. It is part of the Hatsumei Hakken Monogatari Zenshuu series which describes the story of various scientific discoveries and inventions throughout history. The 1983 book focuses on discoveries related to magnetism and electricity.

In future Japan, in a time when android housekeepers have become commonplace, society strictly abides by the Three Laws of Robotics, which all androids must follow. Under the influence of the Robot Ethics Committee, androids are treated the same way as lesser technology, such as household appliances. However, a minority with an adoration for androids exists, categorized as android-holics, and are shunned by the general public. Rikuo Sakisaka was raised to accept society's precept about androids, and is perfectly aware that they are not human. That is, until the day he discovers a strange message buried within the activity logs of his household android, Sammy. This leads him to Eve no Jikan, a cafe with only one rule that its patrons must adhere to: there must be no distinction made between humans and androids. Curiosity drives Rikuo to learn more about the shop, and he attempts to unearth the reason behind Sammy's peculiar behavior.

In 2060, in order to solve various supernatural crises, the World Organization selected elite agents from all over the world to form a crisis bureau. The Dangerous Situation selected the elites of the elite to form an ace squad, named the Phantom. Three years ago, in a task of receiving treasures, due to the gullibility of the captain, Hyway, the Phantom Squad was attacked by the Derek Squad, and almost all of them were killed in action. Hyway himself was planted by Derek and fell into the cliff. However, the target treasure, the Immortal Stone, accidentally entered into Haoyuan's body, bringing him back from the dead, gaining the ability to manipulate time, and possessing super powers such as time static and time reversal. Our protagonist has lived as a fugitive from then on. Haoyuan didn't want to face the past, and chose to remain anonymous, leading a plain life, and guarding Gu Xiaoxi, the sister of his comrade-in-arms. But God’s will, a blue virus appeared in City Y, and the infected person’s skin appeared blue, then spread all over the body little by little, and eventually died. And Gu Xiaoxi was also infected. In order to break the blue virus incident and save Gu Xiaoxi, Hyway returns to the crisis situation. With the sexy and capable secret agent Yu Jie-Xia Rou, the quirky genius Loli-Tong Xiaoxiao, and the second-biggest gangster-Zhan Peng and other weird celebrities make a makeshift to form an alternative phantom team. And our legendary story begins here. (Source: Youku.com, rough translation)

Time flies by; Hiroyuki and Akari are 12th-graders now. Both of them and their friends have grown up gradually in someway, physically or mentally, but one of their best friends is missing: the lifelike android Multi. To their surprise, Multi is brought to their campus again without notice, yet she is no longer the same Multi they have known. (Source: ANN)