In the middle of the 21st century, powerful individuals with superhuman strength appeared all across the world. These people who wore flashy clothes and performed incredible feats in the name of peace became known as heroes—symbolic figures of the nation they came from. In Japan, 14-year-old middle school student Teru Momijiyama is widely known by her secret identity as Japan's hero, Shy. As a young, timid girl, Shy is a fairly new hero with a lot to learn. She struggles with self-confidence and questions if she is worthy of the hero title. Even though she is unsure of herself, Shy works hard to save people and do the right thing. As new, powerful threats reveal themselves, Shy must cooperate with heroes around the world all while learning what it means to be a hero.

My Melody arrives on Earth much to the surprise of her rival Kuromi. Together with one of the junior high school students, Yumeno Uta, they decide to protect the dreams of the people with the help of magic.

In the bustling and futuristic city of Heartland, a young boy named Yuuma Tsukumo has a dream that everyone his age wants to achieve—earning the title of the greatest duelist! Sadly, due to his lackluster dueling skills, this dream is far from achievable. But when the school bully, Ryouga Shark Kamishiro, splits the key given to him by his father into two pieces, he inadvertently sets Yuuma on a collision course with his dream. Retaining one half of the key, Yuuma begins a duel with Shark, but soon realizes that his inexperienced skills are no match for him. In a sudden turn of events, Yuuma's key repairs itself, and the Door of Destiny'' appears before him. Using the key to open it, Yuuma is greeted by an alien by the name of Astral—a being only he can see. The bewildered Yuuma soon learns that his memories have been divided into 100 Number Cards, all of which he must retrieve. However, he is also not the only one looking for them. Bombarded by these revelations, Yuuma, alongside Astral, must defend the world from the upcoming threats that loom over Heartland City—regardless of any divine intervention that may occur.

Kaori Sasaki—a member of Uchihama Academy's Astronomy Club—confesses to Sou Akiyama, but later that evening, she dies in a tragic road accident. Her friends and fellow club members mourn her death in a local hospital. Yet she shows up to school the following day, and no one senses anything amiss. The day finishes without any unusual incidents, and the group of friends plans for the upcoming cultural festival. Suddenly, the room is shaken by an unnatural earthquake. Everyone splits up to investigate—except for Nagisa Hanamiya, who stays behind. As everyone leaves, Nagisa notices that the odd relic-like cube that she was toying with starts emitting a strange blue light. Meanwhile, Sou stumbles upon an unconscious, naked girl lying in a pool of water. Ushinawareta Mirai wo Motomete follows the Astronomy Club's increasingly bizarre adventures—from dealing with ghosts to quelling unrests between student clubs. All the while, they unravel the circumstances behind the sudden appearance of a new transfer student.