Yukiteru Amano is a shy middle schooler who regularly keeps track of what he does in his daily life by writing down all of his activities on his phone—a digital diary. Despite having no friends at school, Yukiteru is frequently seen talking to his supposedly imaginary friends Deus Ex Machina, the god of time and space; and Deus' servant, Mur Mur. One day, Yukiteru wakes up and discovers that certain events of his day are preemptively displayed on his cellphone. While initially dismissing it as a coincidence, he slowly realizes that the incidents written in his phone actually take place in the near future. After spending the day benefiting from this new asset, Yukiteru learns that his classmate Yuno Gasai possesses a similar diary. As the two team up to defeat an odd pursuer and head back to their respective homes, Deus Ex Machina explains that they—alongside 10 other contestants—have been drawn into a survival game whose victor will become the deity's successor. With no other options, Yukiteru and Yuno must use their cellphones—now called Future Diaries—to survive this unforgiving battle royale.

In the distant future, humanity has been driven to near-extinction by giant beasts known as Klaxosaurs, forcing the surviving humans to take refuge in massive fortress cities called Plantations. Children raised here are trained to pilot giant mechas known as FranXX—the only weapons known to be effective against the Klaxosaurs—in boy-girl pairs. Bred for the sole purpose of piloting these machines, these children know nothing of the outside world and are only able to prove their existence by defending their race. Hiro, an aspiring FranXX pilot, has lost his motivation and self-confidence after failing an aptitude test. Skipping out on his class' graduation ceremony, Hiro retreats to a forest lake, where he encounters a mysterious girl with two horns growing out of her head. She introduces herself by her codename Zero Two, which is known to belong to an infamous FranXX pilot known as the Partner Killer. Before Hiro can digest the encounter, the Plantation is rocked by a sudden Klaxosaur attack. Zero Two engages the creature in her FranXX, but it is heavily damaged in the skirmish and crashes near Hiro. Finding her partner dead, Zero Two invites Hiro to pilot the mecha with her, and the duo easily defeats the Klaxosaur in the ensuing fight. With a new partner by his side, Hiro has been given a chance at redemption for his past failures, but at what cost?

The Soul Translator is a state-of-the-art full-dive interface which interacts with the user's Fluctlight—the technological equivalent of a human soul—and fundamentally differs from the orthodox method of sending signals to the brain. The private institute Rath aims to perfect their creation by enlisting the aid of Sword Art Online survivor Kazuto Kirigaya. He works there as a part-time employee to test the system's capabilities in the Underworld: the fantastical realm generated by the Soul Translator. As per the confidentiality contract, any memories created by the machine in the virtual world are wiped upon returning to the real world. Kazuto can only vaguely recall a single name, Alice, which provokes a sense of unease when mentioned in reality. When Kazuto escorts Asuna Yuuki home one evening, they chance upon a familiar foe. Kazuto is mortally wounded in the ensuing fight and loses consciousness. When he comes to, he discovers that he has made a full-dive into the Underworld with seemingly no way to escape. He sets off on a quest, seeking a way back to the physical world once again.

In their teenage years, few things can hurt people more than the heartaches that come with unrequited love. Such is the case for Natsuo Fujii, who has found himself entranced by his school's ever-cheerful teacher Hina. Deflated by this unreachable desire, Natsuo humors his friends and attends a mixer. There he meets Rui, a girl whose lack of excitement rivals that of himself. After bonding over their mutual awkwardness, Rui takes Natsuo to her house and asks him to have sex with her, hoping that the experience will stop her friends from treating her like a clueless child. With his hopeless feelings towards Hina still on his mind, Natsuo hesitantly agrees. Equally unfulfilled by their first times, the two decide to part ways as strangers. However, before he even has a chance to process this experience, Natsuo's father drops a major bombshell: he is getting remarried, and his new wife Tsukiko Tachibana is coming over now to meet Natsuo. As if that was not enough of a shock, her daughters—and, in turn, Natsuo's new sisters—are Hina and Rui Tachibana, the woman he's in love with and the girl with whom he shared his first night. Now, Natsuo must come to terms with the feelings he has for his step-siblings as his eyes open to a darker side of love.