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 steals the three units from Infant Island but is thwarted by Fairy Mothra, Moll and Lora's pet, and fails to retrieve the proper triangle for her sword (each power unit will only work for a specific sword). Moll and Lora end up with a unit that transforms Moll's sword.

Shortly after the Elias sisters faceoff, a meteor shower brings to Earth a huge meteor that disrupts gravity near it, as a family watches. The next day, a teenager called Shota, 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, discovering the essence of dinosaurs, and realizes that a great evil has been released. King Ghidorah, a three-headed space monster who visited Earth in its past and is thought to be responsible for the destruction of the dinosaurs, returns with the captured children to a secluded spot near where the meteor crashed, trapping them in a huge, pulsating organic dome.

Thankfully, at Moll and Lora's calling, Rainbow Mothra arrives and begins to battle King Ghidorah, but the three headed demon's ancient powers render all of Mothra's attacks useless and the King of Terror proceeds to easily dominate Rainbow Mothra, who only just escapes. Later, Moll and Lora encounter Ghidorah, who infects Lora with its evil by staring into Lora's eyes. Under Ghidorah's spell, Lora attacks Moll and attempts to drag them both into the dome. Fairy Mothra flies down towards the dome and saves Moll before she falls into it. Belvera, intrigued by Ghidorah's arrival, gets too close to the dome and is dragged inside by serpent beings. The monster then wreaks havoc in the city.

Meanwhile, Moll and Fairy Mothra encounter Shota, who has discovered that his brother Shuehei and sister Tamako are among the many children trapped inside the dome. Moll tells Shota about Ghidorah's plan to use the children's life force to feed upon. She convinces him to accompany her and meet their only hope, the recovering Rainbow Mothra. Moll and Rainbow Mothra communicate telepathically, discussing their options. It is agreed that Rainbow Mothra cannot defeat Ghidorah in its current form and so it is decided that he must travel to a time when the dinosaurs still walked the Earth, and when the three-headed dragon had visited from space for the first time, then less powerful, to feed upon the Earth's life-force. Rainbow Mothra turns into Aqua Mothra and, with Moll giving the creature all of her powers, the massive insect turns into Light Speed Mothra and breaks through the boundaries of time and travel to confront Ghidorah, some 65 million years in the past.

Moll gives Shota her sword and asks him to go inside the dome to find Lora, and to convince her to use her powers to help Mothra. After Shota reluctantly agrees, Moll languishes and, with her powers totally depleted from helping Mothra time-travel, falls into a state of suspended animation, her body taking on the appearance of frosted glass. Shota allows Ghidorah to capture him so he can find Lora in the dome. There, Lora encounters a worried Belvera, who tells her that Ghidorah plans to destroy the Earth. Lora takes the triangular unit that Belvera had and uses it to transform her sword. Still under Ghidorah's spell, the two fairies engage in a sword fight, with Belvera begging Lora to see reason and to work with her, but to no avail. Shota finds Lora, but she attacks him and attempts to stab him with her sword. Belvera warns Lora not to do it as Shota reminds her that she loves children deeply. Soon, Ghidorah's spell breaks and Lora falls into Shota's hands, her sword then combining with Moll's.

Belvera finally realizes that the Elias triangle represents the three of them, uses the last remaining triangular unit to transform her sword, and then combines her sword with both Lora's and Moll's. Using the new superpower sword, she attempts to break open the dome as Lora recovers. Light Speed Mothra appears in the Age of Dinosaurs and turns back into Rainbow Mothra. Another fight between her and Ghidorah takes place. After originally holding the advantage, Rainbow Mothra is badly wounded. The dome shakes violently and realizing that Rainbow Mothra is losing the battle, Shota asks Lora to use her powers to help the creature. As Lora sings, Rainbow Mothra energizes and manages to immobilize Ghidorah long enough to pick it up and drop it into a nearby volcano, but not before a severed piece of Ghidorah's tail burrows itself into the ground. The volcano erupts with Ghidorah in it, destroying the monster. Rainbow Mothra is hurled out of the exploding volcano, crashes to the ground and dies.

Back in the present time, Ghidorah and the dome disappear, freeing the children and the fairies. Shota reunites with Shuehei and Tamako and they join Belvera and Lora as they sadly kneel by the body of Moll, unsure how they can save her. Back in the past, three Primitive Mothra larvae arrive and wrap the body of Rainbow Mothra in a time-capsule cocoon. Back in the present, Belvera expresses concern to Lora, noting that if Ghidorah is really destroyed, the current course of events would have changed. Suddenly, Ghidorah appears in the sky amidst a massive fireball. This is the other Ghidorah which grew from the severed tail of the creature killed by Rainbow Mothra in the past. The new Ghidorah starts to capture children again. Meanwhile, Belvera convinces Lora to join her in battle, and the two distracts Ghidorah with Fairy Mothra.

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. Another battle takes place, and this time, Ghidorah is no match for his opponent, who slices Ghidorah's wing off and then disintegrates the monster. Armor Mothra then communicates with Belvera and Lora, telling them to join their powers and, using the sword, to bring Moll back to life. The fairies do as they are told and, as a result, the sword vanishes and Moll revives, as Lora and Belvera smile. The reunion between the three sisters is short-lived, as Belvera calls for Garu-Garu and flies off. All the children are released once again and reunited with their parents. Shota, Shuehei, Tamako and their parents watch as Moll and Lora ride away with Fairy Mothra, and Armor Mothra, now transformed as Eternal Mothra, flies into the sunset.