Jun Kobayashi operates as both pilot and navigator aboard the resurrected Space Battleship Yamato. A member of the Earth Defense Forces, he actively contributes to the ship's reconstruction before its recommissioning. His deep personal investment fuels a fierce protectiveness, leading him to physically confront Susumu Kodai in the engine room, mistaking the new captain for a spy and revealing his instincts and initial lack of recognition.

Assigned as a primary Yamato pilot, he flies the advanced Cosmo Pulsar fighter craft and occasionally maneuvers the battleship itself. Confidence marks his flying skills, carrying himself with noticeable pride echoing previous elite pilots. His personality reveals impulsive reactions and a flirtatious side, particularly evident in interactions with crewmate Maho Orihara.

During the mission to escort the Third Emigration Fleet, Kobayashi launches into combat against hostile forces. His role expands to navigation during critical maneuvers. Tension flares with combat chief Kamijo, sparking verbal clashes requiring executive officer intervention. Despite this rivalry, he contributes significantly to defensive actions near black hole BH199, participating in counterattacks protecting evacuation ships. His character development shows a gradual shift from individualistic behavior toward functioning within the crew structure.

Kobayashi's technical expertise is evident through his involvement in rebuilding Yamato, especially its engines. Engineer Tasuke Tokugawa formally introduces his pilot background to Kodai. He maintains a competitive spirit throughout operations, reflecting the high standards of Yamato's historical fighter corps while adapting to new challenges.