Professional baseball player Kenji “Ken” Sato returns to Japan despite being close to winning a championship in America. Reporter Ami Wakita speculates that Ken’s sudden return is due to family matters, but in reality, it is to fight kaiju as the giant superhero Ultraman, a role he reluctantly takes from his father, Professor Sato. After battling the monster Neronga, Ken feels unappreciated and frustrated, remembering his missing mother, Emiko.
Dr. Onda, chief officer of the Kaiju Defense Force (KDF), harbors a grudge against Ultraman and kaiju. During a transport mission, the team is attacked by the bird-like kaiju Gigantron, and Ken leaves a game to fight it. Gigantron loses consciousness atop a secret package, which is an egg that hatches into a baby Gigantron. Ken, who becomes the baby’s guardian, names her Emi and struggles to balance his superhero duties, baseball career, and raising Emi, refusing help from his estranged father.
Ken seeks advice from Ami, who tells him that parenthood, though challenging, can be rewarding. After an incident in Tokyo where Emi escapes, Ken injures her shoulder while trying to save her and finally reaches out to his father for help. Professor Sato helps heal Emi and aids Ken in raising her, leading to a reconciliation between father and son.
Onda reveals his plan to use Emi’s echolocation to find and destroy the kaiju island, justifying it as a necessary action to protect humanity after losing his family in a kaiju incident. At a family cabin, Ken and his father bond over their shared experiences as parents and Ultramen. However, Emi enters a pupal stage, and the KDF attacks, injuring Sato. Ken places his father in a healing tube, and Emi hatches with wings, flying toward her birth mother’s call.
The KDF attacks Ken’s home, destroying his AI assistant Mina and causing Sato’s tube to disappear into the sea. Ultraman tracks Emi to Tokyo Bay, where they face a mechanized Gigantron. Realizing it is a cyborg and not just a machine, Ultraman, with help from Ultradad (Sato), fights the KDF-controlled Gigantron. Onda transforms a KDF craft into a giant mecha and battles the heroes, blaming Ultradad for his family’s death. Onda is ultimately defeated but triggers a self-destruct sequence, which Ultraman contains to prevent further damage.
Later, Ken, who has matured through these experiences, is interviewed by Ami. He reflects on his family and shares a voicemail from his mother expressing her hopes for reconciliation. Ken and his father, with Emi and Gigantron’s help, find the kaiju island. In a mid-credits scene, Ken receives a call from his mother, Emiko, who reveals she is stranded on Ultraman’s home planet in Nebula M78.