Subaru Marita is the son of Robert Marita, a wheelchair-bound university professor and former U.S. Army lieutenant who served in Vietnam. His Japanese mother, a nurse who met Robert during his post-war hospitalization, died during his childhood. As a young microbiologist, Subaru joins a Tsukuba Institute research expedition to Vietnam to study a Halley's Comet meteorite. Before departure, his father gives him a harmonica, hoping Subaru might locate Lamina—a mysterious green-haired woman Robert encountered in Vietnam two decades prior—and return it to her. Investigating the meteorite site in the jungle, Subaru discovers Lamina in an abandoned temple; she appears ageless, unchanged since Robert's meeting. Subaru convinces her to return to Japan with the team for study.

Subaru's relationship with Yumi Torauma, daughter of the expedition's industrialist financier, fractures due to her jealousy over Lamina. Yumi's father opposes their relationship, favoring his subordinate Goyō Yasui as her suitor. After a physical confrontation with Yasui at the airport, Subaru focuses on Lamina, insisting his interest is purely scientific. In Japan, Subaru assists in studying Lamina's extraterrestrial origins and her green powder, which induces rapid growth. When Lamina is targeted by Zamba—an agent sent to eliminate her for defying orders to destroy humanity—Subaru takes her to an isolated dam on Mount Washidaka. During the ensuing confrontation with Zamba, Subaru and Yumi reunite and witness Lamina transform and battle the agent.