The advertising director of Pacific Pharmaceuticals, frustrated with the low ratings of their sponsored TV program, seeks a more sensationalist approach. He orders his staff to Faro Island to capture King Kong for exploitation. As Godzilla re-emerges, a media frenzy generates with Pacific looking to capitalize off of the ultimate battle.

Mining engineer Shigeru investigates the disappearance and death of his fellow coworkers when prehistoric nymphs are discovered emerging from the mines. After an attack on the local village, Shigeru heads deeper into the mines only to make a more horrifying discovery in the form a prehistoric flying creature. Soon a second monster appears as the two converge in Fukuoka.

At the turn of the century, all of the Earth's monsters have been rounded up and kept safely on Monsterland. Chaos erupts when a race of she-aliens known as the Kilaaks unleash the monsters across the world.

A submarine expedition to salvage the remains of Mechagodzilla is thwarted by a massive dinosaur named Titanosaurus. An Interpol investigation leads biologist Ichinose to uncover the work of Dr. Mafune and his mysterious daughter Katsura. Aligned with the Black Hole Aliens, Katsura's life becomes entwined with the resurrected machine.

Reporter Goro Maki stumbles upon scientists conducting weather experiments on Sollgel Island in the South Seas. He discovers the island is inhabited by giant mantis and a woman named Saeko who's been cast away since the death of her father. The pair soon find a helpless infant monster that Godzilla must adopt and learn to raise as one of his own.

The Futurians, time-travelers from the 23rd century, arrive in Japan to warn them of the nation's destruction under Godzilla. They offer to help erase Godzilla from history by preventing his creation. With Godzilla seemingly gone, a new monster emerges as the Futurians' true intentions are revealed.

The U.N.G.C.C. (United Nations Godzilla Countermeasure Center) recovers the remains of Mecha-King Ghidorah and construct Mechagodzilla as a countermeasure against Godzilla. Meanwhile, a giant egg is discovered along with a new monster called Rodan. The egg is soon found to be none other than an infant Godzillasaurus.

Journalists Ichiro Sakai and Junko cover the wreckage of a typhoon when an enormous egg is found and claimed by greedy entrepreneurs. Mothra's fairies arrive and are aided by the journalists in a plea for its return. As their requests are denied, Godzilla arises near Nagoya and the people of Infant Island must decide if they are willing to answer Japan's own pleas for help.

When an underhanded pharmaceutical company goes to a remote tropical island to steal King Kong for advertising purposes, they get more than they bargained for when the gigantic ape attacks an unsuspecting village and an enormous octopus.

Ichiro Miki is a child living in the industrial district of Kawasaki, where his parents' constant struggle to make ends meet often leaves the schoolboy alone. Constantly teased by a bully nicknamed Gabara, his only friends are toy consultant Shinpei and fellow classmate Sachiko. Ichiro turns to escapist dreams of Monster Island where he befriends the equally bullied Minilla.

Gaira, a humanoid sea beast spawned from the discarded cells of Frankenstein's monster, attacks the shores of Tokyo. While the Japanese military prepares to take action, Gaira's Gargantua brother, Sanda, descends from the mountains to defend his kin. A battle between good and evil ensues, leaving brothers divided and a city in ruins.

As supernatural events and monster attacks rock Japan, the military and government look to be overwhelmed. Three intrepid young investigators—two pilots and a reporter—take it upon themselves to study these unexplained phenomena in order to inform and protect the public. With allies and science aiding them on their journey, the trio must separate myth from history as they explore the greater mysteries of these occurrences: are they unrelated, or is this barrage somehow a portent of even worse things to come?