Kouji Kabuto returns to Japan after previous battles against Dr. Hell and the Mycenae Empire. Having studied UFO technology abroad, notably at NASA, he pilots the TFO (Terrestrial Flying Object), a compact reconnaissance saucer he personally designed and built. His mission is peaceful first contact amidst increasing UFO sightings.

Joining the Space Science Laboratory, Kouji meets Daisuke Umon (Duke Fleed). Skeptical of Duke's warnings about the hostile Vegan Empire, Kouji attempts direct communication with approaching Vegan saucers. This triggers a dangerous confrontation, forcing Duke to reveal his alien prince identity and deploy Grendizer, witnessed by Kouji.

Initially fighting in the lightly armed TFO, Kouji battles Vegan forces. The TFO proves inadequate against powerful Saucer Beasts and is destroyed. Kouji then designs and pilots the advanced Double Spazer, a jet-like aircraft with superior weaponry. This new machine docks with Grendizer to provide flight capabilities, transforming Kouji's role from reconnaissance to active combat support for Duke.

Kouji's personality retains earlier traits like impulsiveness, stubbornness, and a hot-blooded combat style, often charging into battle. Yet, he shows growth from past experiences, demonstrating greater willingness to heed advice and strategically retreat. His technical expertise and courage make him a vital ally to Duke.

His relationship with Duke evolves from friction and rivalry into deep mutual respect and friendship. Kouji provides unwavering support for Duke's mission to protect Earth. He also bonds with others at the Space Science Laboratory and the Makiba ranch, including encouraging Hikaru Makiba in her pilot development. Later, he encounters Maria Fleed, Duke's sister, and a mutual romantic attraction develops.

Following the Vegan Empire's defeat and King Vega's downfall, Kouji bids farewell as Duke and Maria depart Earth to rebuild their home planet Fleed.