In a post-apocalyptic world overrun by alien-crafted "Machine Lifeforms," humanity is preparing for its last stand. Forced to retreat to the Moon for safety, humans are pinning their hopes on a group of man-made androids known as YoRHa soldiers. Led by the all-purpose battle android YoRHa 2-gou B-gata "2B," the group will fight to take control of the Earth back from its invaders. As war against the machines rages on, the YoRHa slowly begin to see the first shards of truth underlying the brutal conflict. Facing the harsh reality before her, the unwavering warrior 2B starts to question her very existence and just how much she must sacrifice for the sake of humanity.

Self-professed "home security guard" Mahiro Oyama has not left his home in years, secluding himself in his room playing erotic visual novels. This depraved lifestyle causes his prodigious sister, Mihari, to worry about his well-being. In hopes of solving this problem, she devises a plan to rehabilitate him back to normalcy. The first part of Mihari's plan is to concoct a medicine that changes her brother's biological constitution into a bona fide female, much to Mahiro's vehement dismay. Stuck in this predicament, Mahiro has no choice but to live out his life as a cute girl until the effect wears off—if it ever does.

A mysterious man by the name of Lee dwells with Aak, Hung, and Waai Fu in the dark alleyways of Lungmen City. Styling themselves as Lee's Detective Agency, they strove to run errands, investigate mysteries, and mediate disputes for their neighbors. Herein lists a few of their actual yet strange cases to go with your tea.

In spite of his best time-leaping efforts, Takemichi Hanagaki continuously fails to prevent the present-day death of Hinata Tachibana, his adolescent love. The adult Takemichi grapples with grief and the ramifications of the Tokyo Manji gang's criminal empire—an unintended product of his timeline meddling. Though the gang once operated under the idealistic Manjirou "Mikey" Sano, it has now been taken over by the malicious Tetta Kisaki and, as a result, has abandoned its original optimistic intent. Despite feeling hopeless, Takemichi travels to the past once again to investigate Black Dragon, a rival motorcycle gang whose actions ultimately lead to Hinata's demise. There, he meets the young Hakkai Shiba, a fellow gang member whose older brother, Taiju, tyrannically rules Black Dragon. When Taiju brutally beats Takemichi in a one-sided street brawl, Hakkai attempts to withdraw from Tokyo Manji in apology—an act that Takemichi must prevent to spare Hakkai a grim future. Through a shared tragedy, Takemichi bonds with Chifuyu Matsuno, establishing a close comradery both boys desperately need. With Chifuyu on his side, Takemichi works to unravel the fates of Black Dragon's members, fighting to create a happy future for his loved ones.