In near-future Japan, Aya Okamura lives alone in an apartment away from her parents. Her mother has worked overseas ever since her childhood, so her aging father Kouji and their cat Mii-san are the only ones left in their family home. After a tiring day, Aya declines her father's invitation for dinner by lying that she is still at work. Yet that very night, she receives another call with sudden news that may bring this separated family closer.

The discovery of a black crystalline mineral known as Originium has accelerated technological advancement in the world of Terra, with its high energy yield allowing people to demonstrate abilities akin to magic called Arts. Large veins of Originium can naturally be found at the sites of Catastrophes, various forms of natural disasters caused by the mineral itself. However, the usage of Originium comes at a price, as there is a high risk of getting infected with Oripathy—an incurable and highly contagious disease. Because nations subject the infected to harsh discrimination, the oppressed begin a dissident movement. Calling themselves Reunion, the rebel faction mercilessly destroys cities, further contributing to the already calamitous nature of Catastrophes. Rhodes Island, committed to treating the infected and uninfected as equals, is a paramilitary pharmaceutical organization believed to be the most advanced in its research for the Oripathy cure. Unfortunately, the person spearheading the project—an enigmatic figure known only as the Doctor—suffers from amnesia, effectively impeding what might be the only hope for the infected to break free from their chains of despair.

Osamu and Youko Sonoyama want more than anything to adopt every child from Soramame House, but the wealthy couple can only pick one due to their increasingly old age. While they contemplate this delicate decision, one child's alluring beauty and gentle soul instantly draw them in. Two months later, the Sonoyamas welcome 13-year-old Hitori into their warm and loving home. However, Hitori's humble and overly polite exterior is merely a masquerade. In reality, Hitori is a carefully crafted character played by identical twins Migi and Dali. For them, being the ideal child of this kind couple is merely a stepping stone to infiltrating a certain quiet town. While dutifully protecting their cover, the twins work toward their true objective: to discover the truth behind a past incident that left them with a burning desire for vengeance.

Tsubasa Oozora loves everything about soccer: the cheer of the crowd, the speed of the ball, the passion of the players, and the excitement that comes from striving to be the best soccer player he can be. His goal is to aim for the World Cup, and to do that, he’s spent countless hours practicing soccer, ever since the moment he could walk on two legs. Now, as he plays for the Barcelona team in a fierce game, it seems as though his dreams are on the verge of coming true. Captain Tsubasa: Road to 2002 tells the story of how Tsubasa climbed his way through the ranks, featuring his roots in the town of Nankatsu as well as his epic journey to master the art of soccer.