Chief Harris, known also as Choichiro Hikari, is an Earth Defense Forces officer, first assigned to a space station. After mysterious luminous phenomena appear in Earth's skies, he transfers to the specialized Science Guard Party, formed to investigate these events. During his return journey to Earth, he meets Ultraman Joneus, an Ultra warrior from Planet U-40. Joneus warns of approaching dangers to Earth and proposes merging their essences to fight this threat. Hikari agrees, enabling him to transform into the giant superhero Ultraman Joneus using a device called the beam flasher when needed, while remaining human otherwise.

Within the Science Guard Party, Hikari serves under Captain Akiyama alongside scientific specialists. His dual existence forces him to conceal his identity as Ultraman Joneus from his teammates while defending Earth against monster attacks and alien invasions. This perilous duty leads to his temporary death alongside Joneus battling the Spirit Parasite. Both journey to Planet U-40 for resurrection. Recovering there, they uncover historical ties between the Ultra People and Earth and aid in repelling the Badel People's invasion, including reclaiming the stolen Ultra-mind technology.

After these events, Captain Daisuke Gondo assumes leadership of the Science Guard Party. Hikari continues his duties under this new command, adapting to evolving threats. The resurgence of the Heller Empire, a renegade Ultra faction led by the banished Heller, targets Earth specifically because of Joneus. Hikari and the Science Guard Party receive the Ultria, an ancient Ultra battleship, to counter this menace. In the conflict's climax, Hikari and his team defy Earth military orders, joining space fleet forces to assault the Heller Empire's Titan Base on Saturn. This campaign involves infiltrating Heller City on U-40 to disable its defenses during the fleet battle. Hikari's secret identity is revealed to his teammates when he transforms to save them from Mac Datar. He then joins seven other Ultra warriors to defeat Heller, who perishes in the destruction.

Following the Heller Empire's defeat, Joneus separates from Hikari. Accompanied by his sister Amia, Joneus observes Earth for months to ensure stability before departing, promising to return if future threats emerge. Hikari's journey spans his evolution from military officer to a merged entity with an extraterrestrial protector, his death and resurrection, his pivotal role in interplanetary conflicts, and his eventual return to a solely human existence.