Please keep everything but personal reactions in spoiler tags, though be warned that you're in danger of having certain things revealed just by being in this thread.
Plot summary for context:
(Viewed at an ~N2 Japanese level, so I got most of it, but I'll note where I feel like I missed a bit of context, and everything is subject to some scrutiny as I'm not fluent.)
In space, the command ship has listened to a recording of Haruo's destruction of Mechagodzilla City, and a verbal fight breaks out between the Bilusaludo leader and the humans. The humans are outraged at the scope of the Mechagodzilla/nanometal plan, while the Bilusaldo leader maintains that it was the only way to defeat Godzilla/rebuild civilization, and wants Haruo brought to justice.
On Earth, all but a few of the small group of survivors have been gripped with increasing religious fervor under Metphies, who encourages the belief that a miracle is the only that saved them from being absorbed by the nanometal (as many of their friends were).
Haruo and the scientist check in on Yuko. Haruo protests she's still alive, but the head scientist states it's merely the nanometal keeping her heart beating; she's brain dead.
Haruo speaks in private with the scientist about the religious fervor among survivors. The scientist points out that they all share one thing in common--they received medical treatment from the human civilization earlier. Haruo remembers that this is true of him as well (the powder he woke up with in the last film). He asks why the scientist has kept silent, but he replies that this isn't the kind of atmosphere where he could safely reveal things. Haruo too has lost favor with the group.
During a group discussion, the scientist posits that Haruo gave up on trying to destroy Godzilla with the nanometal because it would mean nothign to win and give up their humanity. Metphies, if I recall correctly, corrects him and says he likely feared what Mechagodzilla would have become in Godzilla's place.
Later in the film, Haruo expresses that a combination of these feelings was responsible for his actions. He does regret that he was unable to make the choice to commit to giving up his humanity, as Yuko apparently was (and in effect this difference of resolves lead to him killing her). So there's quite a bit of effort to not render things completely black and white.
Haruo speaks with Metphies in private and confronts him with the idea that the Mothra civilization's medical treatment saved them rather than a miracle. Metphies says he thought as much, but that the current resolve of the crew is necessary to call in their god. Haruo is both confused and outraged, and above all questions why, if Metphies really believes he has a way to defeat Godzilla, he allowed all the sacrifices up to now. Metphies discusses the necessity of both the Bilusaludo technology and human psychology as triggers. Most of all, Haruo's own resolve to defeat Godzilla will be necessary, and Metphies has been waiting for it to come to a boil, though at this point Haruo himself no longer believes humanity has any way to win.
Haruo talks to the scientist again, believing Metphies to be insane. More pressingly, the Bilusaludo have taken over the command ship and are demanding Haruo be brought in. He says it's better Haruo disappear for the time being, and one of the twins has offered to stow him somewhere away from the group.
In a small room hidden in the side of the cliffs, the twin expresses her belief that "winning," for Haruo, would simply be staying alive. She offers to "connect" with him and strips. She struggles to remove his spacesuit, and he turns her down. She leaves.
A bit later, the--I believe--other twin, appears by Haruo's side, having successfully removed the top part of his spacesuit while he slept, and he realizes this is the one who treated him in the last movie. She strips and this time they embrace.
I think this was a different twin each time--and I hope that's true, because it's suitably weird--but to be honest I wasn't paying attention to any of the elements that separated them earlier, so it might have been the same one. Mea culpa. Around this time, though I forget which of the two twin scenes this takes place in, Haruo reveals that yet another reason for his attack on Mechagodzilla was the knowledge that his humans had already lost long ago, and he was unwilling to sacrifice this new civilization for it.
Meanwhile, the other twin has snuck into a religious alter room used by Metphies. He's conducting a prayer simultaneously with the Exif leader on the ship, and the two are communicating telepathically. As he finishes, he telepathically calls out to the twin, asking her to show herself.
She asks why he hasn't revealed his telepathy before, and he says concealing it was necessary to earn the trust of the Earthlings and Bilusaludo. She tries to escape, but he catches her and shows her a vision of Ghidorah, which terrifies her and alerts her twin (in Haruo's room) to danger. When her twin awakes, she says the name "Ghidorah," which alerts Haruo that Metphies is up to something. Haruo has gone though his own nightmare invloving Metphies just prior.
Shortly after, Mepthies begins one more group prayer. He feeds everyone soup and discusses how though it has been fully consumed by his followers, it continues to exist as part of them. However, unlike soup, living beings like them are able to make their own choices. He leads them in a rallying cry to Ghidorah, and this time, at the height of his followers' fervor, simultaneously with a prayer aboard the command ship, he touches his amulet to the green communication stone he's been holding, and three dragon heads begin to emerge, visible only through shadows. They slice the followers to bits.
Above the command ship, a hole in space has opened, and this time a visible dragon head begins to wrap itself around the ship. No one inside can get any readings from it. It coils around the ship and destroys it, killing everyone inside.
On Earth, things have gone haywire. Three holes have opened in the sky, and dragon heads have begun to emerge from each. Around this time, Godzilla, who's been slumbering since his battle with Mechagodzilla and regaining energy, awakens. The humans all gather at a lookout atop the cliffs.
Haruo, knowing that Metphies is responsible, runs off alone to find him. The rest of the group watches Godzilla begin his battle with Ghidorah. Ghidorah gives off no life signature and no energy signature, confusing the humans from Haruo's group. Godzilla fires at Ghidorah and he reflects the beam. Godzilla's swipes move right through his necks. As Ghidorah's heads siphon heat from Godzilla, which seems to completely disappear, the scientist speculates that Ghidorah exists in and is moving the energy to a separate plane of reality.
Haruo reaches Metphies and finds the other twin tied up, but alive. Metphies has gouged out one of his own eyes and replaced it with the amulet, which he's using to interact with (control?) Ghidorah. He looks at Haruo and launches a psychic assault against him. He walks him through the past, showing all of the ways humans have heralded their own end with technology, and reveals that Ghidorah is the being that destroyed the Exif planet, after which all survivors have willingly embraced him as a form of inescapable entropy. Embracing a nihilist view, they now endeavor to willingly offer worlds to him. He wants Haruo to embrace this as well, though--other than this somehow being necessary to anchor Ghidorah--I'm unsure how; it's possible I missed something.
The twin at the lookout and the scientist have meanwhile gone off to Mothra's egg together, and use it as a psychic conduit to intervene in Metphies' assault. Mothra, in silhouette, flies into Haruo's visions and shatters a plane Haruo and Metphies are in as Metphies discusses entropy over images of the atomic bomb.
Among the psychic visions Metphies continues to assault Haruo with are the visages of his dead friends asking him why he threw away their hard work and chose not to avenge them. He also reveals that the elderly members of the command ship whose ship exploded in the first film, including Haruo's grandfather, chose their fate, and that Metphies himself supplied them with explosives before their ship took off. Though I suppose whether this actually happened or was merely Metphies trying to get at Haruo could be up for debate.
Haruo remembers his parents' decision to name him after spring, and a flower charm they gave him as a very young child, and this combined with the revelation about the ship of the elderly survivors pushes him into rejecting Metphies fully. He's able to break free long enough to gouge out both the amulet and Metphies' remaining eye. His connection to Ghidorah severed, Ghidorah becomes locked into our plane of reality, and Godzilla is able to physically injure him. He kills the heads and fires atomic beams through each of the worm holes, causing them to explode.
Dawn breaks and Haruo sits with Metphies as Metphies dies.
A great span of time passes. The very small group of remaining survivors integrates with the human civilization on Earth. The twin Haruo slept with is pregnant with his child (and apparently married to him) and takes him to see some flowers blooming outside the cliffs--the first spring he remembers seeing, even though it's his namesake (haru=spring). The scientist calls Haruo over to take a look at one of the fallen Vultures. Haruo claims there's no way it can work again, but the scientist has gotten it running by taking a sample of nanometal from Yuko's body (still kept in its comatose state by the Mothra civilization). With this, they can begin to rebuild a technologically advanced society along with the humans on Earth.
Haruo holds his right eye and is confronted with a momentary vision from Metphies, claiming that time is their ally. (I.e., progress will eventually lead them to destruction again.)
Haruo stows away from the group and takes Yuko's body. The twin he isn't married to catches him and asks what he's doing. He asks her if Godzilla's scary, and she says he is. He asks her if she hates him (more literally, if he's despicable), and she isn't sure. He talks about how he may lose, but can at least make the choice to lose. She says she doesn't understand and Haruo replies that's fine. He either says, at this point--I missed the beginning of this sentence--that he fears he may eventually come to understand their way of life (letting go and living) or that she may understand his perspective one day, and leaves with Yuko. I hope it's the former, because that's more interesting; in addition to recognizing the threat of the nanometal/technology's return, on some level he's still too proud to live in the shadow of his grudge.
He flies with Yuko's body in the reactivated vulture and charges directly toward Godzilla, knowing he'll die. Godzilla fires on the Vulture and destroys it.
Post credits, a group of children (I believe of mixed heritage, between Haruo's group and the Mothra civilization) burn small rope decorations in front of an effigy that resembles the Vulture, offering prayers to be safe from things like sickness, bug bites, etc. One of the now-elderly twins looks on. A priestess encourages the children to let the fire burn away their fears.
Edit--The summary here is also completely accurate, and seems to be from a higher-level Japanese speaker, though it's spread out over several 4chan posts. But if you clicked just to get an overview of the film, you can combine details from both and get a pretty complete picture.
I like that a number of believable motivations are offered for each character, and indeed tension and layered character conflict have been the strengths of these films and Gen Urobuchi's writing, as far as I know it, in general. Multiple reasons are given for Haruo's decisions, all plausible, and I think each rings true in some way. In particular, elements like his guilt over having betrayed Yuko in some way, who was comfortable with resolving to change her definition of humanity in line with the Bilusaludo's goals, are a nice touch. Ghidorah is also an absolute nightmare. I don't think he's ever been scarier. The film seems to land as him being a scientific anomaly beyond current understanding, but he really does feel in presentation like a Lovecraftian eldritch horror. The scenes building up to his fight with Godzilla are genuinely creepy.
However ... I think the second film remains the strongest of the trilogy. Compared to the Bilusaludo's arguments in the second movie, the goals of the Exif are rather too transparently villainous--unless you're really swayed by pat nihilism, and even then, there isn't a compelling reason to accept their voluntary embrace of entropy over survival. I found the combat sequences more exciting in the second movie as well. Haruo's more or less done changing by the time his movie rolls around, only getting to show the resolve he had already arrived at by the end of the second (to just live, though in the end he still does bare his pride and grudge to some extent).
Finally, this has the Gen Urobuchi curse. Or at least what seems to be a common weakness between these movies and Madoka Magica, which is the only other work by him I've seen or read. Namely that, while he's excellent at building tension, and presenting layered character motivations and letting them play off of one another, it amounts to very little of weight. Much like that series, for all the believable tension he mines, by the final act it shows itself as having little to offer in terms of prompting us to reconsider our world. There's a pep talk in here on surviving, and letting things be, but anything applicable to your own perspective on life or modern fears is about as shallow as could be.
That still puts it above the vast majority of other hard sci-fi takes on Godzilla though (to the extent that the series largely breaks down into approaches that prioritize social/political commentary, spectacle kitsch, and hard sci-fi, with the latter having by far the weakest track record, I think). The second entry, which is the tightest piece of self-contained sci-fi between the three, and which places those conflicting character motivations that are a genuine strength of the writer's on center stage, is the one I'm likely to come back to in the future, and makes a dip into the trilogy worth it on the whole. And by no means did I have a bad time watching this movie, even though I wish, as I'll probably always with with its writer, it were able to focus its tension and character-writing into a sharper point.
Oh--I've read a few Japanese reviews since. One reviewer took issue with being unable to become invested in the anime trilogy in general due to how far removed it is from reality (when the kaiju genre is really premised on one fantastic element dropping into the ordinary), and called Urobuchi strong medicine, so ... I suppose, really, if you've been turned off on these movies on premise, nothing is going to change here. I do agree with the sentiment that the film is held back somewhat on offering anything of genuine substance due to its completely fictional setting (and likely simply the particular weakness of its writer that is his inability to focus interesting character interactions into any kind of challenging or compelling theme), which is why I tend to prefer both the more grounded and complete kitsch Godzilla entries over the hard sci-fi ones, but we've already had a number in the franchise that eschew any kind of reality, and none have been half as competently executed as this run was, so it's a point I identify with somewhat but think has little ground to stand on speaking of the series or genre as a whole.
I give it two spooky Ghidorahs out of three. I like, but don't love, the anime trilogy, and think the second entry is the strongest part. The third has its strengths too, but is subject to Urobuchi's usual weakness with endings that fail to imbue all of the layered and interesting character tension with anything of thematic weight. It is still, on the whole, the most competently executed and interesting hard sci-fi take on Godzilla we've gotten to this point.