Moll, Lora, and Belvera, the Elias sisters are at odds again. Belvera seeks the secret power of their ancestors, tiny triangular power units that transform the sisters' small daggers into powerful swords. She fails to retrieve the proper triangle for her sword, each power unit will only work for a specific sword, but Moll and Lora end up with a unit that transforms one of their swords.
Shortly after the Elias sisters face-off, a meteor shower brings a strange object to Earth, a huge meteor that disrupts gravity near it. As it crashes to Earth at night, a family watches. The next day, the oldest of the children, a teenage boy, plays hookey from school, and goes to investigate the object. Meanwhile, school children on playgrounds and around the nearby city begin to mysteriously vanish as a huge shadow passes overhead. Moll and Lora examine the remains of the crashed meteor, realizing that something has escaped, and sensing a great evil has been released. Grand King Ghidorah, a space monster who visited Earth in its past, returns with the captured children to a secluded spot near where the meteor crashed, trapping them in a huge, pulsating organic dome. Belvera, intrigued by Grand King Ghidorah's arrival, and hoping to use him for her own ends, gets too close to the dome, and is drawn inside. Later, Moll and Lora encounter Grand King Ghidorah, and Lora is infected with the monster's evil as she stares into one of its eyes. Lora attacks Moll, under the evil influence, and Fairy falls from the sky with Moll and Lora, saving Moll before she is also trapped in the dome. Lora joins Belvera inside the dome, where the captured children are screaming and huddling together, terrified. A battle between Belvera and Lora takes place, with Belvera begging for Lora to see reason and to work with her, but Lora is still being influenced by the spell of Grand King Ghidorah.
Meanwhile Moll, riding Fairy, encounters the teenage boy, and tells him about Grand King Ghidorah. She explains that Grand King Ghidorah needs the childrens' life force to feed upon. She convinces him to accompany her and meet their only hope, Rainbow Mothra, who is now recovering from a battle with Grand King Ghidorah. Moll and Rainbow Mothra communicate telepathically, discussing their options. It is agreed that Rainbow Mothra cannot defeat Grand King Ghidorah in its current form-- it is too powerful-- and so it is decided that Rainbow Mothra must travel back in time to a point where Grand King Ghidorah was not so powerful, to a time when the dinosaurs still walked the Earth, and when Grand King Ghidorah had visited from space for the first time to feed upon the Earth's life-force. Rainbow Mothra turns in to Aqua Mothra and then with Moll giving Aqua Mothra all of her power, the massive insect is able to turn into Light Speed Mothra and break through the boundaries of Time and travel backward to confront Grand King Ghidorah, some 65 million years in the past. Moll, her power totally depleted helping her friend time-travel, falls into a state of suspended animation, her body taking on the appearance of frosted glass. Light Speed Mothra appears in the age of the dinosaurs and turns back into Rainbow Mothra. Another fight between Rainbow Mothra and Cretaceous King Ghidorah, Grand King Ghidorah's younger form, takes place, and Rainbow Mothra, nearly dead, manages to immobilize Cretaceous King Ghidorah long enough to pick it up and drop it into a nearby volcano, but not before a severed slice off Cretaceous King Ghidorah's tail burrows itself into the ground. Rainbow Mothra is hurled out of the exploding volcano, where prehistoric Mothra Larva cover him in a time-capsule cocoon in which the injured Rainbow Mothra will sleep for many millions of years, and metamorph into a new form.
Back in the present Grand King Ghidorah roars in outrage as it disappears from existence. The children are released, and the boy joins Belvera and Lora (now recovered from her infection by Grand King Ghidorah, thanks to the love of her sisters) as they kneel by the body of their sister Moll, unsure of how they can save her. Suddenly Grand King Ghidorah appears in the sky amidst a massive fireball. This is the other Grand King Ghidorah which grew from the severed tail of the Cretaceous King Ghidorah killed by Rainbow Mothra in the past. The tail regenerated over time into a full-grown Grand King Ghidorah. The new Grand King Ghidorah starts to capture children again, when suddenly the time-capsule cocoon explodes from a mountain, and Rainbow Mothra emerges, this time as Armor Mothra, a formidable version with armour plating all over it. Yet another battle takes place, and this time Grand King Ghidorah is not even a close-to match for Armor Mothra, who first slices Grand King Ghidorah's wing off, and then proceeds to completely disintegrate the monster. Armor Mothra then communicates with Belvera and Lora, telling them to join their powers, and so using the sword bring Moll back to life. The touching reunion between the sisters is short-lived, as Belvera calls for her winged henchman, Garu-Garu, and flies off, promising more conflicts between the sisters, who disagree over how the Elias should interact with (or have power over) Humankind. The children are reunited with their parents, and Armor Mothra transforms into his final form, Eternal Mothra, and flies into the sunset.
The film grossed around $7,000,000 at the box office.