Pre-Evolution of Life: A race of aliens called the Precursors arrive on Earth through dimensional rifts called Breaches. They attempt to build a civilization on the cooling world, but are forced to return to their home dimension by evolving temperatures. However, in their rush to leave, they leave behind one of their UFOs.
Mezozoic Era: A superspecies of DNA-absorbing dragonfly known as Meganulon appears. Several Tyrannosaurs, while attempting to pursue prey, are trapped in a massive cave system containing a radioactive hotspot. They evolve into Gojirasaurs, working in packs and feeding on radiation, using excess as a growth hormone. All dinosaurs are subsequently wiped out by a meteor, except for the Gojirasaurs.
The Ice Age: Early humans have the ability to channel mana, the Earth's lifeforce, into magical spells. They found a great empire known as Atlantis. Atlantis was reportedly a utopia, with such mastery of magic that it had little to envy of modern cities, but its downfall came eventually at the hands of the Gyaos. A magical experiment gone wrong accidentally created several 10-meter-tall bat-bird hybrids called Gyaos. Reproducing at an exponential rate, they attacked Atlantis and killed hundreds. Eventually, the Atlanteans used the same process that created the Gyaos to create Gamera, a far larger and stronger turtle-like monster wielding the element of fire. Gamera wiped out the Gyaos, but a couple eggs remained. The Earth's soul then unleashed two more monsters: the demonic butterfly Battra, and his angelic twin Mothra. The two sunk Atlantis, entombing the elemental monsters and destroying the Atlanteans' magic research so that the Gyaos could not be recreated. Mothra guided the survivors into a hunter-gatherer lifestyle before dying and leaving behind an egg.
1945: Robert Oppenheimer invents the atomic bomb.
1954: An atomic bomb is tested on Lagos Island. Unknown to anyone, a pair of Gojirasaurs, a brother and a sister, live on the island. The nuke causes them to grow to gargantuan sizes, with the sister (dubbed "Godzilla I") driven mad and the brother (dubbed "Godzilla II") left comatose by the painful transformation. Godzilla I attacks Tokyo and levels it completely, proving immune to all conventional weapons. However, the scientist Daisuke Serizawa has invented a substance known as micro-oxygen. Meant to be a medicinal aid, it instead dissolves oxygen particles. His fiance convinces him to use it against Godzilla I while she sleeps in the harbor. Aided by a military team, Serizawa detonates a micro-oxygen mine that kills Godzilla I, but he allows himself to be vaporized by the compound as well in order to prevent his creation being used against humanity.
1984: Godzilla II finally awakens from his coma. Seeking revenge for his sister, he makes his own attack on Tokyo, destroying assembled JSDF forces. They eventually deploy an anti-nuclear plane known as the Super-X, which manages to temporarily knock Godzilla out using cadmium shells. However, an accidental Soviet missile launch causes a radiation storm that revives Godzilla, and he makes short work of the Super-X. An alternative plan is hastily put together, and a magnetic wave transmitter is used to lure Godzilla to the volcanic Mount Mihara, where planted charges are used to bury him in the crater. Erika Shiragami is fatally buried in rubble shortly afterwards. Her father, geneticist Genichiro Shiragami, discovers roses growing from her body and, concluding they are her reincarnation, takes them with him. However, when they begin to die, Shiragami splices them with Godzilla cells to make his "daughter" immortal.
1989: A botched terrorist plot frees Godzilla from Mount Mihara, spurring the roses to grow into a massive monster called Biollante. Godzilla mistakes Biollante's cries for his sister's and seeks her out, attacking her when her true nature is revealed. He sets her on fire and she escapes into the atmosphere in the form of spores. Shiragami collaborates with the JSDF to create "Anti-Nuclear Energy Bacteria", which will weaken Godzilla by reducing his radiation reserves. Godzilla tries to attack Osaka, but psychic Miki Saeguasa forces him to turn away and he is successfully infected with the ANEB. Biollante returns in a more powerful form as the terrorists attempt to kidnap Shiragami to make more ANEB. He escapes in a jet as Godzilla again reduces Biollante to spores. For unknown reasons (perhaps she really is the reincarnation of Erika?) the spores carried Shiragami in his jet into space with her. Godzilla, weakened by the ANEB, swims out to sea.
1992: Mothra's egg is discovered and brought to Japan as not just Godzilla, but a larval Battra, awaken. En route to Japan, the two monsters convene on the egg and battle each other as the egg hatches. Mothra's twin priestesses the Cosmos tell Miki Saeguasa about Atlantis and the origins of the monsters while Mothra enters her imago form. The two moths unite to battle Godzilla in Yokohama, subdue him, and begin carrying him back to Mount Mihara. However, he regains consciousness and mortally wounds Battra. Heartbroken, Mothra drops them both into the sea, and Godzilla is forced to observe someone grieving over the death of her sibling. However, this time, the killer wasn't the humans. Godzilla swims away from Japan rather than continue his attack, and Mothra and the Cosmos head into space to avert the impact of the meteor Gorath. Meanwhile, Shiragami and Biollante are sucked into a black hole. Biollante's plant cells are destroyed by the intense gravity and her Godzilla cells are fused with a being of living crystal, creating a crystalline Godzilla known as Spacegodzilla. Shiragami's fate is unknown.
1993: The UN finishes construction of Mechagodzilla, a giant robotic duplicate of Godzilla planned to be used to kill him. Meanwhile, the JSDF discovers an infant Gojirasaurus and brings it to Miki Saeguasa's institute for psychic children. Miki and the children bond with "Baby Godzilla", but JSDF commander Takaaki Aso plans to use him as bait for Godzilla so Mechagodzilla can kill him. Miki protests, citing Godzilla's lack of attacks since the previous year, but was overruled. The operation was a total disaster, with Mechagodzilla destroyed. To stave him off, Baby Godzilla was surrendered to the adult beast, and they traveled to Baas Island to start a family.
1994: Spacegodzilla arrives on Earth and kidnaps Baby Godzilla, assembling a crystalline fortress in Fukuoka. Godzilla attempts to pursue him, but is held back by the JSDF. However, with Spacegodzilla proving the bigger threat, Godzilla is reluctantly allowed to reach Fukuoka. He battles Spacegodzilla and, with the aid of UN forces, is able to kill him and free his son before returning to Baas Island without further attacks. This set a major legal precedent, with a "Do Not Provoke" order eventually filed for Godzilla so long as his only coming ashore is to battle malevolent kaiju- essentially, "don't hit us and we won't hit you".
1995: Miki Saeguasa's psychic power begins to fade. Three Gyaos eggs hatch and the resultant creatures wipe out an entire village. Fifteen-year-old Asagi Kusanagi discovers a mysterious amulet on an atoll, inadvertently linking herself to Gamera, the Atlantean fire monster, who resembles a giant turtle. Gamera awakens and destroys two of the Gyaos, but is shot down over the ocean by the JSDF. The last Gyaos consumes the corpses of its brethren, becoming a massive Super Gyaos that attacks Tokyo. Godzilla uses his nuclear energy to revive Gamera, who travels to Tokyo and kills the Super Gyaos after a lengthy battle, after which a Do Not Provoke is filed for him. Godzilla's nuclear heart briefly becomes unstable, but Gamera uses mana to stabilize it.
1999: The UFO left behind by the Precursors is discovered. It activates, drawing power from the sun, and flies to Shinjuku. However, maser weapons are used to cut open the hull, and when its computers reveal it to have hostile intentions, a group of psychics disable it.
2000: A weapon known as the Dimension Tide, capable of firing artificial black holes, is developed. A test firing accidentally brings the Meganulon back from the past. The swarm attacks Godzilla and absorbs his DNA before injecting it into their queen, Megaguirus. She mutates into a giant monster and fights Godzilla, who manages to eventually kill her. However, numerous eggs remain. The Meganulon spread across the globe, but local police keep them to manageable levels and they slowly become just another animal.
2013-2020: K-Day. The Precursors open a Breach in the Pacific Ocean and begin sending through genetically engineered Breach Kaiju to conquer Earth. It starts with two sent per year, but the number increases each year. Godzilla and Gamera kill some of them, but they can't be everywhere. The UN funds the Pan Pacific Defense Corps to pilot giant robots known as Jaegers against the Breach Kaiju. Jaegers are controlled via a telepathic link known as the drift, a process that will kill almost any one person who tries it. Hence, Jaegers are piloted by duos. Between Godzilla, Gamera, and the PPDC, Breach Kaiju rarely even reach cities. Fatalities drop further when former Jaeger pilot Stacker Pentecost becomes the PPDC's marshall. With the world united in the face of adversity and equipped with advanced Jaeger technology, it seems a new golden age is on the rise.
2020: Mothra failed to stop Gorath and it impacts South America, causing massive geothermal upheaval. Everyone within a thousand-mile radius of the crash was killed instantly, and worldwide, massive tremors killed hundreds of thousands. The Breach was destabilized, causing several global EMPs. Almost everyone requiring medical aid of some form died, and all resistance against the kaiju was crippled. The Meganulon overran Japan, Russia, the Koreas, and Europe, although the dictator of Russia managed to deprive them of control over his country by nuking it into oblivion. It is now an inhospitable wasteland, and in Europe, one of the only refuges against the Meganulon is London, now twice its original size and overrun with crime. The Gyaos burst out of Australia, in months reduced it to a wasteland, and invaded through the Pacific. Mexico and the West Coast have fallen to them, and they have conquered all the rest of Asia. China, India, Mongolia… all gone. Some have survived in these death-nations, but the numbers drop day by day. The Precursors finally closed the old Breach, but almost immediately opened a new one in the Indian Ocean twenty times its predecessor's size. Madagascar was swallowed by it, and it unleashes dozens of Breach Kaiju into Mozambique by the week. They have so far conquered up to the Sahel region, despite the efforts of the Canadian-African Union, a united war front of Canada and every remaining African county. They wage a never-ending war against the Breach Kaiju, but with no Jaegers, the most they can do is hold the line, and with the Breach Kaiju getting stronger and stronger, their ability to do such a thing becomes rapidly in doubt. And what of the world's brave defenders? Gamera self-destructed to save Hawaii from the Gyaos, in the process warding it against further attacks. Baby Godzilla vanished without a trace, while the Jaegers sit in the Tokyo Shatterdome with no power. And the great Godzilla sacrificed himself to drag Knifehead, the last kaiju to emerge from the old Breach, into a volcanic vent, burying them both alive. This looks to be the end of civilization… but Tokyo has not fallen to Meganulon. The PPDC has defended it and is retaking the surrounding areas, and Stacker Pentecost has a plan to fix the world.
AN: I figured I'd been doing a bunch of Calvin, but not much Zilla. So here we go! And no, Godzilla vs King Ghidorah did not happen in this 'verse, due to the different future. Mechas were still constructed, but using Jaeger technology instead of tech from Mecha-King Ghidorah. EDIT: Neither did Godzilla vs Destoroyah, for that matter, due to the Super Gyaos attacking Tokyo during the same year and, with a stray shot, accidentally wiping out most of the larval Destoroyahs in Tokyo Bay. Advent of Legion also didn't happen because [SPOILERS], and because of it the Mana Cannon wasn't used and so Awakening of Irys didn't happen either.