Descendants of the Shobijin that lived on Infant Island in the 1960's, this new generation, like their predecessors, are the envoys of Mothra. Sent to see Shin'ichi Chujo, the doctor who was part of the original expedition to Infant Island in 1961, the Shobijin warn against humanity's disrespect for the dead by using the bones of the original Godzilla in order to construct Kiryu. With Shin'ichi is his nephew, Yoshito Chujo, who is a mechanic on the Kiryu project, and the Shobijin aim their plea directly at him, announcing that Godzilla's bones must be returned to the sea where they belong. However, their request falls on deaf ears as Yoshito refutes that Kiryu is their only protection against further attacks from Godzilla. The Shobijin then announce that if their request is fulfilled that Mothra will protect Japan in Kiryu's place; however, if the request is ignored, than Mothra will once again be an enemy of humanity. With that final warning, the Shobijin take their leave with Mothra.

As days pass, Shin'ichi tries his earnest to fulfill the Shobijin's request, even getting council from the prime minister on the matter; unfortunately, all agree that as long as Godzilla threatens Japan they can't dump the Kiryu project.

Eventually, after a series of attacks that includes the death of Kamoebas and the destruction of a US nuclear submarine, Godzilla emerges in Japan. It's discovered, far too late, that the creature has been attracted by the bones of his ancestor, explaining his earlier attacks in 2002 and his appearance in Japan. Upon Godzilla's arrival, Shin'ichi's grandson, Shun Chujo, sets out to construct a giant replica of Mothra's emblem using the desks at his school. Upon completion, the boy's efforts are rewarded by the arrival of Mothra, who then does battle with Godzilla. Sadly, Mothra is no match for Godzilla in a one-on-one confrontation and so Japan's prime minister deploys Kiryu to aid the country's savior. Unfortunately, even Mothra and Kiryu's combined efforts are not enough to defeat the King of the Monsters.

Meanwhile, on Himago Island, the Shobijin awaken the offspring of Mothra who hatch from their egg revealing twins. The larvae disembark from the island to the Japanese mainland where, after a long battle alongside Kiryu that costs the Imago Mothra its life, are victorious against Godzilla. With victory finally achieved, the Shobijin issue their final warning as they announce that no human should tamper with those who have passed, as Kiryu and Godzilla return to their watery confinement in the Japan trench, never to be seen again.