Morgana operates as the primary antagonist, initially presenting himself as ICPO director Michael F. Morgan, Inspector Zenigata's superior. His true identity reveals him as the leader of the secretive Morgana sect, a cult with tendrils reaching back to figures like Oda Nobunaga, Toyotomi Hideyoshi, and Adolf Hitler, all pursuers of the powerful Fujin artifact. Created by Roman scientists who later fled to Japan and allied with bandits to form the Fūma ninja clan, Fujin possesses the destructive power to generate black holes.

Ruthlessly eliminating anyone obstructing his goals, Morgana conceals a clan crest—a shield with a coiled snake—on his forehead beneath a mask, his visible expressions limited to shifts between anger and manic glee. He commands armored guards who sometimes pose as officers and utilizes advanced weaponry, including concealed body armor capable of deflecting blades and bullets. His methods involve intricate traps and technological manipulation, such as escalating electrical currents to interrogate captives, causing their clothing to disintegrate.

His plot centers on stealing a gold Buddha statue, taken from a Nazi cache and intercepted from Lupin III, which contains a key component leading to Fujin. During this heist, he seemingly kills Zenigata, though the inspector later resurfaces after an undercover Fūma ninja, Asuka, placed him in a death-like coma. Morgana captures Asuka and her sister Maya, leveraging them to access the Fūma clan's secrets. His pursuit culminates in a temple confrontation with Lupin and his allies. After Asuka breaks his mask, exposing his eye, Morgana retreats deeper into the structure, laughing maniacally as it collapses around him.