After losing both parents in a fatal plane crash, teenager Ryuuichi Kashima must adjust to his new life as the guardian of his younger brother Kotarou. Although Ryuuichi is able to maintain a friendly and kindhearted demeanor, Kotarou is a reserved toddler still too young to understand the reality of the situation. At their parents' funeral, they are approached by Youko Morinomiya, the stern chairman of an elite academy, who decides to take them under her care.
However, there is one condition Ryuuichi must fulfill in exchange for a roof over their heads and enrolment in the school—he must become the school's babysitter. In an effort to support the female teachers at the academy, a babysitter's club was established to look after their infant children; unfortunately, the club is severely short-staffed, so now not only is Ryuuichi responsible for his little brother, but also a handful of toddlers who possess dynamic personalities.
Hayato Hayasugi (his last name is a pun on the words for "too fast") and other children will serve as conductors to pilot the Shinkalion. The Shinkalion robots are various models of real-life Japanese bullet trains (shinkansen) that transform into robots to fight an unknown evil to protect the safety and peace of Japan.
The children must work together with the adults of the Shinkansen Ultra Evolution Institute (SUEI) to defeat a monster that looks like a jet black bullet train.
While cleaning his house, eight-year-old Elon finds a summoning device and scooter left behind by his brilliant scientist grandfather. While riding the scooter and wearing the summoning device on his wrist he gets into a dangerous situation. Just then, the Archean necklace his grandfather left behind starts lighting up and summons an ancient Infinite Warrior (a Metalion) named Leo. Leo saves Elon from danger, and develops a liking for Elon. The newly reawakened Leo is appalled by the unruliness of humans and is saddened that Earth’s energy had long been depleted. Leo explains to Elon how he’s a Infinite Warrior and used to be his grandfather’s friend. Leo asks Elon to help him find all the remaining Archean Stones to restore the Earth’s energy. Elon designs a stone detector and uses it to begin his journey with Leo. The pair set off in search of the stones scattered around the world.