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.

Yuuta Hibiki wakes up in the room of Rikka Takarada and notices two things: he has no memories, and he can hear a mysterious voice calling his name from a nearby room. On further inspection, he finds a robot—which introduces itself as Hyper Agent Gridman—behind the screen of an old computer. Much to Yuuta's surprise, Rikka cannot hear Gridman, nor can she see the ominous monsters looming over a thick fog as it envelopes the town outside. Another giant monster materializes in the city and proceeds to wreak havoc. Amidst the confusion, Yuuta is once again drawn to the old computer and merges with Gridman. Suddenly, he appears in the middle of the battle and is forced to fight the monster. Together with Rikka and fellow classmate Shou Utsumi, Yuuta forms the Gridman Alliance to defeat the monsters plaguing the city and find whoever is responsible for their emergence.

OZ, a virtual world connected to the internet, has become extremely popular worldwide as a spot for people to engage in a large variety of activities, such as playing sports or shopping, through avatars created and customized by the user. OZ also possesses a near impenetrable security due to its strong encryption, ensuring that any personal data transmitted through the networks will be kept safe in order to protect those who use it. Because of its convenient applications, the majority of society has become highly dependent on the simulated reality, even going as far as entrusting the system with bringing back the unmanned asteroid explorer, Arawashi. Kenji Koiso is a 17-year-old math genius and part-time OZ moderator who is invited by his crush Natsuki Shinohara on a summer trip. But unbeknownst to him, this adventure requires him to act as her fiancé. Shortly after arriving at Natsuki's family's estate, which is preparing for her great-grandmother's 90th birthday, he receives a strange, coded message on his cell phone from an unknown sender who challenges him to solve it. Kenji is able to crack the code, but little does he know that his math expertise has just put Earth in great danger.

On the eve of a junior high school's cultural festival, Typhoon No. 8 slowly approaches the isolated Okinawan town of Naha. A mysterious girl wearing a strange necklace suddenly appears alongside the storm, catching Shuuichi Azuma off guard. After getting into a fight with his best friend Kenta Saijou over his decision to quit the baseball team, Azuma notices the same girl standing atop an electrical tower when lightning strikes, cutting power to the school and causing her to tumble down below. Unwilling to stay in the same room as Saijou, Azuma runs off to rescue the strange girl as the storm intensifies.