A decade ago, mankind witnessed the deadly potential of weapons caused by the Great War. To avoid another catastrophe, governments worldwide have resorted to espionage to fulfill their agendas. In the Din Republic, Lily is an enthusiastic young girl who aspires to become a spy and serve her nation. However, she begins to doubt her abilities, as she struggles to perform well academically. Lily's passion is reignited when she is offered provisional graduation by joining the spy team Lamplight, which she eagerly accepts despite the enigmatic nature of the opportunity. Upon arriving at her destination, Lily is surprised to find six other girls waiting there, all of whom have faced their own academic difficulties as well. A mysterious man named Klaus soon appears and reveals they must complete an "Impossible Mission": to infiltrate the Galgad Empire after just one month of training. Although skeptical, the girls eventually agree to work together under Klaus' guidance—as this might be their only chance to prove their worth as spies.

Mahiru Shiina is worthy of her nickname "Angel": she is a divine beauty loved by all, and she excels in both academics and athletics. Shiina lives in an entirely different world from Amane Fujimiya, her next-door neighbor. Despite living so close together, they have never spoken once. But their silence is broken when Fujimiya spots Shiina gloomily sitting on a swing amidst a heavy rainstorm and lends her his umbrella. When Fujimiya catches a cold the next day, Shiina wishes to return the favor for the umbrella by nursing him back to health. Believing that this would be their first and last interaction, he silently appreciates her kindness. However, Shiina—who can not help but worry about Fujimiya's lack of tidiness and proper nutrition—begins to cook and clean for him. As the unlikely pair spend time together in Fujimiya's apartment, they explore the true nature of their relationship and the gentle emotions that emerge from it.

Childhood friends Tomo Aizawa and Junichirou "Jun" Kubota do everything together, whether it be training or just enjoying a fun day out. Anyone would think that these two are best friends for life. The only issue is that the tomboyish Tomo is in love with Jun, but he regards her like a brother. At the start of their first year of high school, Tomo confesses her feelings to Jun. However, her rough mannerisms and lack of hesitance to throw a punch do nothing to sway Jun's heart. Realizing that he will remain indifferent to her affections unless she does something about it, Tomo must find a way to knock some sense into Jun and open his eyes to what is right in front of him.

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.