Long before the present era, the violent Grongi tribe terrorized the peaceful Linto people. A single Linto warrior, empowered by a mystical belt known as the Arcle, transformed into the warrior Kuuga and successfully sealed away the Grongi and their leader. In the year 2000, an archaeological excavation in Nagano, Japan, unearths the stone belt and the sealed tomb, inadvertently breaking the ancient seal. The Grongi, monstrous creatures able to disguise themselves as humans marked by tattoos, are reborn. Viewing modern humanity as the descendants of the Linto, they resume their brutal "game" of ritualistic murders.

A multi-talented and perpetually optimistic young man named Yusuke Godai feels a mysterious pull toward the excavated site. When a Grongi attacks the police station where he is being questioned, Yusuke dons the ancient belt. The belt fuses with his body, allowing him to transform into Kamen Rider Kuuga, though initially only in a weak, incomplete form known as Growing Form. Witnessing the grief of a young girl who lost her father to the monsters solidifies Yusukes resolve to fight, not out of hatred, but to protect the smiles of others. He takes on the name Kuuga and allies himself with the Tokyo Metropolitan Police, particularly the determined and sharp-minded Inspector Kaoru Ichijo, who becomes his closest confidant and strategist.

As Yusuke battles the Grongi, which the police officially designate as Unidentified Lifeforms, he discovers that his form can change based on his will and the situation. Alongside archaeologist Sakurako Sawatari, who translates ancient Linto inscriptions, Yusuke learns to access several forms: the balanced Mighty Form, the swift and jumping Dragon Form which uses a staff, the hyper-sensitive Pegasus Form which manifests a gun, and the heavily armored Titan Form which wields a sword. The story is structured in three distinct arcs. The first arc introduces Yusuke, his sister Minori, and his support network, including his doctor Shuichi Tsubaki, as he masters these four forms while the police establish a specialized task force to combat the escalating threat.

The second arc intensifies as the Grongi become stronger. After a near-fatal poisoning, the Arcle revives Yusuke, allowing him to access upgraded Rising forms, which are silver-armored versions of his existing powers with enhanced weapons. This evolution comes at a cost, as the belt fuses deeper into his nervous system, causing him pain. The narrative delves deeper into the rules of the Grongis game, known as the Gegeru, which dictates the order and methods of their killings. As the weaker Grongi are killed off, more powerful generals appear, forcing Yusuke and the police to employ heavier weaponry and the high-performance BeatChaser motorcycle to keep pace with the escalating violence.

In the final arc, the nature of Kuuga himself becomes a source of suspense. Yusuke learns that the power of Kuuga is not purely of the peaceful Linto but is connected to the Grongi. As he struggles to control a dark, black-armored Ultimate Form that emerges when his emotions run high, the Grongi lord N-Daguva-Zeba finally appears. Daguva is a sadistic mirror of Kuuga, possessing similar shape-shifting abilities and overwhelming power. Realizing that only the Ultimate Form can match Daguva, but fearing he will lose his humanity and become an even greater threat than the Grongi, Yusuke prepares for the final confrontation. He extracts a promise from Ichijo to kill him if he loses control.

The series concludes with Yusuke assuming the Ultimate Form, powered by his gentle nature rather than hatred, to battle Daguva on a snowy mountain pass. The two equally matched warriors fight until they exhaust their power, reverting to their human forms and nearly killing each other. Though Yusuke survives, the final battle leaves its marks. Three months later, Daguva is confirmed dead, and the Grongi threat is over. Staying true to his wandering spirit, Yusuke Godai bids farewell to his friends and sets off on a journey across the world, bringing his promise to protect smiles with him wherever he travels.