The millennium era of the Godzilla films is officially over with the christening of the new Japanese era with Emperor Heisei taking a much-deserved retirement. In hindsight it is an interesting era as it is the only era so far where a vast majority of the films had no continuity with each other at all. Yes the Showa era had only loose continuity at best, mostly held in place by returning monsters, but it was still there and the Heisei saga had very tight continuity or the events of one film often directly led it to the next one. The millennium series could best be described as anthology based, several of the films have continuity with the original film but nothing else, with only one direct sequel to the prior film. Inspired by this thread and a friend's timeline, here is the first part of my effort.
This would be hypothetically what would've happened if I had full control over the series and was fully aware of what it looked like in our timeline. I will give myself some restrictions though. I cannot add in any movies in at least this initial draft, maybe I'll do a follow-up draft where I can add in unmade films. I can however take material from anywhere I want so long as it is made to fit in one of the finished movies.
I will also be assuming I don't produce a box office bomb that kills off the series prematurely.
Godzilla 2000 -
First changes I would make for sure are exactly what the American cut did to the film. Tighten up some of the long shots, change up the music, add in a little levity with the dialogue, and maybe tweak Orga's design so we can have a more dynamic fight (such as lightening the arms so we can have a bit of a better tooth and claw fight given the final costume couldn't move its fingers). But by and large it's a good reboot that is simple to understand. One key thing to remember is most every character in the film assumes they are operating in a purely scientific world in line with most of the Heisei series. This movie mostly abides by that, but tid bits keep cropping up suggesting this isn't the case.
Godzilla is tracked by Yuji Shinoda, his daughter Io, and Yuki Ichinose in the Godzilla Prediction Network, following his rampages. It's established he roams through Japan and several other countries sporadically, but Japan far more. His origins are still a mystery since it was discovered in 1954 but it is assumed to be the second of its kind after the original was seemingly killed the oxygen destroyer. Most assume it's a mutation brought on by nuclear testing. Crisis Control Intelligence uncovers an anomaly in the deep ocean they tried to mine for energy but it turns out to be a dormant UFO of the Millennian species. The Millennian UFO absorbs all the information at CCI headquarters while Godzilla keeps chasing it across Japan. The GPN discovers is a colony vessel from an Empire that is trying to populate the planet by using regenerator G1, which Shinoda had been researching, to adapt. When aliens are suddenly attacked by Godzilla after destroying much of CCI's weapons, they use a regenerator on themselves untested and turn into the monster Orga. Godzilla destroys it after a long battle departs after killing CCI Chairman Katagiri.
If I wanted to make a few more changes I actually would add continuity in at least some reference to the 1954 film to establish the scientific hypothesis this Godzilla is the second of its kind. Additionally play in the scientific ambiguity about Godzilla as the Big G in this continuity is a poorly studied enigma. Reference Odo island (perhaps by making Shinoda's parent an islander, likely Shinkichi Yamane, effectively making him this continuity's version of Kenichi Yamane from GvsDestoroyah) to add in a bit of the mythological aspect. This will be a re-occurring theme in this continuity where it is ambiguous whether Godzilla has truly scientific origins or is a mythological being. One could even play it to the implication of the latter by having regenerator-G1 go erratic for anything by Godzilla, implying there is more than just cellular biology at work.
One thing I could consider adding to imply other monsters have attacked before is an opening sequence similar to Godzilla: Final Wars, showing several movies in this continuity such as the original Godzilla film, Mothra, the two Toho Frankenstein movies, Varan, and Rodan.
Godzilla vs. Megaguirus -
This film to me is the most inexplicable and inexcusable reboot. You would barely have to change any of the back story and any lines in the film to make it in continuity with Godzilla 2000 and many people already assumed it was given the suit used. So I'm doing that now. Some changes needed other than having a few of the CCI and GPN characters showing up, is perhaps CCI being responsible for making Dimension Tide by reverse engineering the surviving UFO technology; but this is a top level secret.
Japan, through CCI, has been secretly reverse engineering Millennian technology to create a massive technology boom. The main human villain is the seemingly charitable politician, son of a WW2 Imperial Japanese general who operated in China whom his son proudly displays in his office and have his employees dress in guard similar to the Imperial Navy (hint hint, foreshadowing), who has been front running this with CCI after he effectively took control post Katagiri's death. He is wanting to exploit the alien technology to allow Japan to get a massive leg up on the rest of the world, with some imperialist notions. A worrying observation Shinoda, who is in the movie as a consultant, makes is how children say the Imperial Navy inspired uniforms of the G-Graspers look "cool" and waving WW2 era flags. Instead of Godzilla being attracted to nuclear power plants and plasma energy, this is actually just a cover story. In reality he's going after places that are reverse engineering Millennian technology and is agitated by the presence of the reverse engineered technology. The underlying motif is those who do not learn from the past or acknowledge it, are doomed to catastrophes or pain.
The movie overall plays more or less the same just with these elements. CCI has created the new subdivision the G-Graspers and new technology to try and kill Godzilla. During a test firing of dimension tide, a Meganulon insect arrives in the present and lays an egg that becomes a whole colony. The colony ravages parts of Tokyo and attacks Godzilla for energy and dimension tide is fired again to try and get them both, but they miss and another monster comes through the portal. Meanwhile the surviving insects feed Godzilla's energy into a massive egg that hatches into their queen Megaguirus. All kaiju converge on Osaka for a battle.
Optimally I would like to put in Rodan as a natural predator to the Meganulon species that came through a second portal (ever notice how only the first one explicitly opens up a wormhole? Fixing that). So the final battle is a big three-way melee to make up for the fight in the movie, which was good but short. In the end however there is one big difference. Instead of getting successfully shot by Dimension Tide, Godzilla shoots down the satellite the moment they start charging up. This again brings in the mystic aspect as there is no physical way an animal (which Godzilla has been repeatedly called despite the GPN insisting this isn't the case) could have known it was up there and posed a threat.
Rodan survived the battle and departs. Godzilla destroys CCI headquarters and stops to roar when it sees the Imperial Japanese poster, burning down that building in particular because of the all Millennian technology (with a shot of the flag and poster of the general burning up), then goes back into the ocean.
A reoccurring theme is some anti-humanism. Not to the effect of being anti-human, but that humanity is not the apex and unaccountable. Every attempt thus far by humanity to use technology to destroy what is seemingly mightier than them, like Godzilla, just causes more problems. excavating the not destroying the UFO before it could drain data lead to Orga, and now Dimension Tide lead to Megaguirus and Rodan while Godzilla lives.
End credits scene of the sea at Odo Island. In a callback to the first movie, the ocean lights up near a boat and an atomic breath that starts as the familiar red-orange of the millennium Godzilla turns white as it shoots into the sky.
Giant Monsters All-Out Attack -
First things first. I got an idea for Ghidorah and Mothra for later so that's why. Changing the roster back to what it was originally. Godzilla's appearance has now changed slightly, with the blank white-out eyes and a white colored atomic breath. The characters notice this. I wouldn't say it's outright the GMK suit, it's still MireGoji, but altered.
Baragon and Varan (taking Mothra's role) are both kaiju that had been previously known (only change being they never were sure if Varan perished) and had been written off as freak mutations or just giant animals. Varan however was venerated as in ancient kami, and that will be the reveal in the movie that these creatures are the real deal and are being inhabited by mystical souls. The old book is used and this reveal comes when Yuri notices Baragon and Varan look almost identical to two of the three guardian monsters in the book, despite the book being hundreds of years old and clearly older than any potential nuclear mutations. The book also contains an illustration from Odo Island that clearly resembles Godzilla, calling it the embodiment of retribution. This brings up the implication Godzilla is not just a nuclear mutation (most had been assuming this in manner of the Heisei films). And particularly, the Guardian monsters are actually being empowered and possessed, on the direction of a mystic, by the spirits of all those Godzilla has ever killed. Godzilla is being driven by the spirits of all those Imperial Japan killed. This will go to show Godzilla is much stronger.
Godzilla returns after a year-long absence amidst a cornucopia of other strange events such as reports of ghostly possession. Even more ruthless than normal, it makes a beeline for Japan after destroying a cruise (nod to 1954's film). Reporter Yuri Tachibana, Yuki Ichinose's protégé at a news outlet that works with the GPN, finds herself wrapped up in a story about mysticism when she is warned by a repentant WW2 veteran that Godzilla is coming for a reason and that defenses made by science will not be enough. Off dialogue by other characters reveals this man claims to be the last surviving shaman and he goes about erecting shrines at three specific areas in Japan. From here he invokes the spirits of all those killed by Godzilla to possess and control three massive yokai monsters into acting on Japan's behalf.
Baragon engages Godzilla in Hokkaido and loses, but manages to hold the line long enough for many humans to escape. Godzilla then battles the G-Graspers across Japan while making his way to Tokyo. A second monster, a returned Varan, attacks him there and they battle across the city. One notable change is Baragon survives his battle with Godzilla, as he did in the original script, and joins Varan in Tokyo. They hold the line until the most powerful Guardian, Anguirus shows up. Instead of just drill missiles, the Gotengo drills ship features in this movie as the G-Graspers trump card.
The three monsters managed to at least damage Godzilla, but even though he is much more powerful they don't seem to die. This is when we get our first outright mystical instance in the series. Varan and Baragon are incapacitated and seem to perish, loading all of their souls' energy into Anguirus to supercharge him. Anguirus manages the fight fairly well and forces Godzilla into Tokyo Bay, until Godzilla grabs him and forcefully exorcises all of the souls within it. They all come spewing out and are soon followed by those inside Godzilla, who releases a massive roar that shatters every piece of glass for miles. It all lights up like a massive aurora and all of Japan feels and overpowering sense of despair and dread. Whatever pain Godzilla has inflicted, they cannot use it to justify forgetting what their ancestors caused others. And they cannot repeat that mistake.
Anguirus becomes aware again, but after looking at Godzilla, calmly just departs. The other two monsters also leave. The Gotengo is then downed after it suddenly acts on its own and tries to kill Godzilla by firing the freezer maser down his throat. Something that came out of the Guardian monsters during the exorcism that did not go into the humans had flown into it. Remember how I said the trio were possessed by all the souls Godzilla had ever killed? Those weren't just human. The ship is possessed by the spirit of Orga and the Millennian, another empire callous about the pain inflicted on others. But its ploy is stopped. Admiral Tachibana lands it and stands on the bow as Godzilla looms over. Having been forewarned ahead of time by Yuri and Shinoda, he discards his Imperial-styled hat, rips the flag off his uniform, and gets on his knees with his head bowed. All the rest of the G-Graspers do the same.
Godzilla roars in the Admiral's face and seemed to charge up its beam, only to fire over his head and rake one big sweep across Tokyo, cleaving Tokyo Tower in two. It shows how much devastation it could have wrought if it really wanted to. The spirits of the deceased had humiliated and humbled Japan. Japan had started back down that dark path but they hadn't devoted to it just yet. This plays into a conversation earlier where the Admiral is asked by his daughter,
"If Japan has all this power to try and destroy Godzilla, what will they do with it after they succeed?"
The implication being imperialism and reckless nationalism might return, this is all very relevant to Japan in the modern day as neo-imperialist ambitions were a very real thing before the 1990s market crash and there's still is a very strong sentiment in Japan to not own up to the atrocities committed in World War II; which has soured their relationship with other Asian countries even to this very day. It's all one big warning, do this again and Godzilla won't stop. Godzilla loses the whited out eyes and heads back into the ocean with the vengeful souls at rest, Godzilla is undefeated.
As an end credits scene, instead of the one we got, we see several computers in a dark room flicker on with the words 'Millennian' filling the screen just like they did in G:2000 (scene cut in US version). Ghosts in the machines of their design, the aliens have been resurrected. This echoes the previous narrative of the last film. Trying to conquer Godzilla by overstepping human boundaries with technology and now mysticism have only made more and more monsters.
*EDIT* Fixed some typos, sorry I was using tablet and autocorrect hit me a few times