The manga Captain Zenigata centers on Koichi Zenigata, the indomitable Interpol inspector whose entire existence is defined by the pursuit of the master thief Lupin III. While Zenigata is a globally respected officer with a sharp mind and a strong sense of justice, his obsession with capturing Lupin has consumed his life, leaving him a lonely, often messy man with little else beyond his mission. Unlike the more comedic and softer portrayal in the anime, this spin-off from the original Lupin III manga presents Zenigata with a snide, malicious, and intensely competitive temperament, where his hatred for Lupin is so profound that he once reflected he could not live in a world without someone to despise. The setting shifts across the globe as Zenigata follows Lupin's trail of heists, from the bustling streets of Tokyo to various international locales, always one step behind but refusing to give up.

The narrative explores the darkly complicated relationship between Zenigata and Lupin. Though they are arch-rivals, a twisted mutual respect exists; Zenigata is often secretly awed by Lupin's genius, and Lupin will occasionally save Zenigata's life, believing the chase would not be the same without him. This obsession drives several notable arcs. In one striking storyline, Zenigata goes so far as to cryogenically freeze himself to continue his chase into the future, though a malfunction traps both him and Lupin in the present. The manga also reveals details of Zenigata's personal history, including a strained relationship with a daughter named Toshiko and a grandson who is a student at Todai University, who once fiercely opposed Lupin's presence on campus. The story concludes on a shocking and definitive note that contrasts sharply with the eternal stalemate of the anime, as Zenigata finally succeeds in his goal by detonating an island with Lupin and his gang on it, killing the thief he had spent his life hunting.