Shin Kusaka, son of N1 research center scientist Dr. Cromwell Collins, received a glowing pendant and the codeword "Thundersub" from his dying father during an alien attack. Entrusted with reaching the N1 facility for humanity's survival, Shin led fellow students there, encountering a mute girl named Anna en route. At N1, the pendant guided them to a hidden chamber housing the advanced warship Blue Noah, which Shin activated by speaking the codeword.

Integrated into Blue Noah's crew under Captain Ei Domon, Shin primarily served aboard the auxiliary submersible Tempest Jr. He proved his leadership coordinating missions to rescue human survivors and assault alien installations. His bond with Anna deepened as he helped her overcome trauma, culminating in a pivotal intervention that broke her catatonic state after a devastating loss.

When Captain Domon suffered mortal injuries in the final battle against the alien command satellite Terror Star, Shin assumed command of Blue Noah. He directed the vessel to successfully prevent Terror Star's collision with Earth. After the conflict, Shin married Anna and together they established an organization dedicated to planetary defense against future extraterrestrial threats.