Corrupt politicians, frenzied nationalists, and other warmongering forces constantly jeopardize the thin veneer of peace between neighboring countries Ostania and Westalis. In spite of their plots, renowned spy and master of disguise Twilight fulfills dangerous missions one after another in the hope that no child will have to experience the horrors of war. In the bustling Ostanian city of Berlint, Twilight dons the alias of Loid Forger, an esteemed psychiatrist. However, his true intention is to gather intelligence on prominent politician Donovan Desmond, who only appears rarely in public at his sons' school: the prestigious Eden Academy. Enlisting the help of unmarried city hall clerk Yor Briar to act as his wife and adopting the curious six-year-old orphan Anya as his daughter, Loid enacts his master plan. He will enroll Anya in Eden Academy, where Loid hopes she will excel and give him the opportunity to meet Donovan without arousing suspicion. Unfortunately for Loid, even a man of his talents has trouble playing the figure of a loving father and husband. And just like Loid is hiding his true identity, Yor—who is an underground assassin known as Thorn Princess—and Anya—an esper who can read people's minds—have no plans to disclose their own secrets either. Although this picture-perfect family is founded on deception, the Forgers gradually come to understand that the love they share for one another trumps all else.

Tomoya Okazaki and Nagisa Furukawa have graduated from high school, and together, they experience the emotional rollercoaster of growing up. Unable to decide on a course for his future, Tomoya learns the value of a strong work ethic and discovers the strength of Nagisa's support. Through the couple's dedication and unity of purpose, they push forward to confront their personal problems, deepen their old relationships, and create new bonds. Time also moves on in the Illusionary World. As the plains grow cold with the approach of winter, the Illusionary Girl and the Garbage Doll are presented with a difficult situation that reveals the World's true purpose.

With Anya Forger successfully enrolled at the renowned Eden Academy, Operation Strix advances to its second phase. To investigate Ostanian politician Donovan Desmond, Anya must either befriend his son Damian or collect eight Stella Stars to become an Imperial Scholar. Fortunately, Anya has already acquired her first star. In celebration, her adoptive father, Loid, decides to fulfill her wish to adopt a dog. During their canine search, Loid receives new orders from his superiors, who have found that a band of Berlint University students is plotting to assassinate Westalis' Minister Brantz using bombs worn by trained dogs. While Loid tries to stop their plans, Anya stumbles upon the terrorists' base of operations. There, she befriends a kindhearted, clairvoyant dog who the family later names Bond. Although the Forgers continue to lead their individual lives in secrecy, the family—with a new fluffy addition—remains united through all of the unusual obstacles thrown their way.

Hana, a hard-working college student, falls in love with a mysterious man who attends one of her classes though he is not an actual student. As it turns out, he is not truly human either. On a full moon night, he transforms, revealing that he is the last werewolf alive. Despite this, Hana's love remains strong, and the two ultimately decide to start a family. Hana gives birth to two healthy children—Ame, born during rainfall, and Yuki, born during snowfall—both possessing the ability to turn into wolves, a trait inherited from their father. All too soon, however, the sudden death of her lover devastates Hana's life, leaving her to raise a peculiar family completely on her own. The stress of raising her wild-natured children in a densely populated city, all while keeping their identity a secret, culminates in a decision to move to the countryside, where she hopes Ame and Yuki can live a life free from the judgments of society. Wolf Children is the heartwarming story about the challenges of being a single mother in an unforgiving modern world.