"Little Jumper" centers on a young protagonist named Haru, a high school student with a unique ability to leap great distances and heights, a power he discovers after a mysterious accident. Haru’s life takes a dramatic turn when he encounters a secret organization known as the Sky Watchers, who reveal that his abilities are tied to a larger, hidden conflict involving other individuals with similar powers. These individuals, referred to as "Jumpers," are divided into factions, each with differing ideologies about how their abilities should be used—whether for personal gain, protection, or domination.

The narrative explores Haru’s journey as he navigates this newfound world, grappling with the moral implications of his powers and the responsibilities they entail. Alongside Haru is a diverse cast of characters, including Aya, a fellow Jumper with a tragic past who becomes both a mentor and a rival, and Kenta, a childhood friend who provides emotional grounding and support. The story delves into themes of identity, power, and the consequences of choice, as Haru is repeatedly forced to confront the ethical dilemmas posed by his abilities and the actions of other Jumpers.

The plot unfolds through a series of escalating conflicts, as Haru and his allies face off against antagonistic Jumpers who seek to exploit their powers for destructive purposes. The Sky Watchers play a pivotal role, serving as both allies and manipulators, often blurring the line between friend and foe. As the story progresses, Haru uncovers deeper secrets about the origins of the Jumpers’ abilities, leading to revelations that challenge his understanding of himself and the world around him. The narrative balances action-packed sequences with moments of introspection, creating a dynamic and engaging storyline that keeps readers invested in Haru’s growth and the evolving relationships between the characters.