The following table is drawn from the Showa Toho timeline established by Chris N. It shows the cities that were destroyed by dai kaiju invasions in the various monster movies, plus the various war targets of the US atomic bombings; the Mysterian invasion; the Muan war; and the various alien-controlled kaiju attacks starting in the 1960's and continuing on and off for the next several decades.

Note: These are the cities Chris listed; for the most part, I am going with this list as I have only seen about six or seven of these films. I have changed the 1962 listing from Hokkaido, as written by Chris, to Osaka, because Hokkaido is actually the island that Tokyo is on, and I believe that I have seen a still from the film where Kong is at Osaka Castle [d'oh! Thanks for that correction, dude! -CN]. There are some non-Japanese locations listed, as the dai kaiju of the Showa Toho Universe did visit places beyond Japan. This is far from a complete list of all places visited.

In the observations listed after the table, I discuss several targets and possible reasons why certain places were targeted. I also briefly discuss the reconstruction of cities and why they always seem to be rebuilt in time for the next film.

Observations:

1) You will see that the cities that were targeted by the US for atomic bombs were never attacked by dai kaiju. As amply demonstrated by Chris, the big guys seemed to develop psychic abilities, not just for communication purposes, but also developed long-distance awareness of threats-both to themselves, and later to the humans they decided to protect-almost as if they could tap into the Force like Jedis from the 'Star Wars' cycle. I propose that is exactly what happened in the case of Hiroshima and Nagasaki. The sudden deaths of 70,000 to 100,000 people, plus the intense radiation from the bombing sites, acted as psychic/physical warnings for the kaiju to play "keep away from there." Furthermore, without actually plotting out atomic test locations on a map and displaying them, they also seemed to give the testing detonation sites a wide berth as well. The radiation affected the dai kaiju from a distance while also encouraging them to keep away from those special hot spots.

2) The subtle psychic emanations from the Odo Islanders attracted Godzilla, who physically embodied their ancient protector-god myth. After arrival on the island, he visits a couple of times before a combination of being repulsed by the islanders' fear and attraction to the angst of the metropolis of Tokyo (reactions to the war, to economic domination by the US, to the American atomic tests) and the yummy nuclear power sources (controlled atomic radiation versus the uncontrolled radiation of the bombing site producing different particles that either attracted him or repulsed him--and he is shown in later movies to be attracted to power plants--even in the different timelines, his biology is still similar enough to want to go to atomic power plants).

It is certainly telling that Tokyo does not receive a kaiju visit for several years after this first appearance of the Kaiju King. When it is visited, there are specific reasons and they are not random chance encounters.
In 1961, Mothra visits Tokyo, but only to rescue the Shobujin priestesses after they were kidnapped by an unscrupulous and greedy American capitalist; she follows them all the way to New York to rescue them, although I am uncertain if New York was damaged or not.
In 1962, King Kong is brought to Tokyo, and Godzilla, using his new 'enemies awareness' psychic abilities, comes to Tokyo to fight the most famous American kaiju.
The reasons for the Dagora "space spores" attacking cities across the world in 1964 was rather straightforward (the giant, single-minded jelly-fish like entities were feeding on any available source of carbon).
In 1965, King Ghidorah visits Tokyo under the control of the Xians.
In 1966, the Gargantuas visit nearby Haneda Airport looking for food, which is as close to random chance as any post-1954 visit is.
In 1967, humans again brought King Kong to Tokyo.
In 1971, Godzilla was summoned to Tokyo by the psychic emanations of young Kenny to fight the Smog Monster Hedorah, produced by man's unthinking polluting of the environment. (Side note: There is a strong parallel to J. R. R. Tolkien's THE HOBBIT here, as the Smog Monster acts a bit like Smaug the dragon. Smaug killed with his flame breath while flying and Hedorah exuded an acid cloud, which killed humans just as quickly while flying. A tall hero killed Smaug/Smog thanks to the intervention of a small person--Bard the Guardsman of Laketown killed Smaug with an arrow thanks to information from small hobbit Bilbo Baggins, who believed that if anyone could defeat Smaug, it would be Bard [and literally, it was the case of a little bird told him the monster's weakness! --GL], while tall Godzilla--by now, a major hero--was psychically summoned by young Kenny, who thought that if anyone could defeat Hedorah the Smog Monster, it would be Godzilla, who somehow fathomed that drawing Hedorah into the humans' electrical trap would prove the monster's weakness.)
In 1972, 1975, and 1999, the visits to Tokyo were all made by monsters under alien control (and other cities were targeted in the 1999 invasion, as well).

3) The first visit to Osaka appears to be random, although it is possible that Osaka had a working nuclear reactor and/or many survivors of the destruction of Tokyo had fled to Osaka. Godzilla and Anguirus picked up on both the psychic emanations of the people as well as the physical yummy snack radiation. (Side note: As evidenced in later adventures, these two kaiju became fast friends and best buddies. While Godzilla worked well, and extensively, with Mothra and Rodan, Anguirus appears to be his best pal and the one he communicates with the easiest.)
The second dai kaiju visit to Osaka was a result of the humans bringing Kong to Japan.
The third visit was only because the Gargantuas were looking for food.

4) Aliens, most specifically the Xians, directed all the attacks by kaiju in the 21st century.

5) The Muan war was fought where the Muans lived, and their undersea/underground domain was destroyed by the actions of the advanced submarine Atragon. (Side note: This is a parallel to the US defeat of Japan with advanced weapons; while the US did not destroy Japan, Japanese society went through a complete upheaval.)

6) The Letchi Island and Solgell Island incidents, as well as the putative events on (the future) Monster Island in Son of Godzilla, simply reflect that this was where some of the dai kaiju were living at the time of the incident.

7) The Mysterians paid the first visit to Mount Fuji (and they were not the last alien invaders to base themselves there). During their studies of human civilization, they discovered that Mount Fuji was a center for Japanese spirituality (somewhat similar to the importance of Jerusalem for Jews, Christians, and Muslims), and decided that it made an excellent symbolic base to take over the world from. The next visit was by a (presumably) alien-controlled King Ghidorah (and again, Fuji made a great symbolic target for anyone observing Earth, especially Japan); and then we saw a hungry, gigantic Frankenstein monster hanging out there.

(Side note 1: In some of the various analogues to the Showa Toho Universe, the Mysterian invasion is actually the Japanese part of the 1951-1952 Martian (Sarmak) invasion depicted in 'The War of the Worlds' by George Pal. As Pal had a heckuva lot bigger budget than Toho, the Toho invaders were forced to be humanoid, and had a lot fewer flying machines. The film itself took longer to be produced as a film subject and was released some years later. But certainly both Mysterian and Martian (Sarmak) invasions would have stimulated a response by the humans to unite against the invaders, and would have led to a tremendous technology increase. This is the premise behind my Alter-NASA Universe, in which space technology goes through tremendous funding increases--followed by a huge increase in the amount of astronauts and cosmonauts--as the world tries to prevent more invasions in the wake of the 1951-52 global disaster, and even take the battle to the invaders themselves!)

(Side note 2: King Ghidorah's first visits to Earth in the early to mid-1960's are analogues to major events in other universes: In the Marvel Universe, Galactus comes to Earth, seeking sustenance, only to be defeated by the Fantastic Four, who were piloted into space by Ben Grimm; and in the Wold Newton Universe, the 'Galactus' incident is really an incursion into Earth's solar system by a Doomsday Machine (similar to the one that was defeated by James T. Kirk of the USS Enterprise in 2267), and that one was defeated by the WNU-equivalent of the Fantastic Four [known simply as 'the Four', as per creative mythographer Dennis Power's theories -CN].
In Godzilla vs. Monster Zero, the highly advanced spaceship was piloted by US-born astronaut Glenn, the Showa Toho Universe's analogue to our timeline's NASA astronaut John Glenn [who is also alleged to have possibly have encountered alien life both in fiction and via "real" universe conspiracy theory --GL]. With his co-pilot, the Japanese-born Fuji, we are provided with double symbolism of both Mount Fuji, and being an analogue of Classic Star Trek's helmsman Hikaru Sulu, as the show was being produced in our timeline at approximately the same time. So, we have the Grimm/Glenn, Ghidorah/Galactus, and Fuji/Sulu cross-dimensional coincidences at this very important juncture in history.)

8) From the onscreen imagery, no city appears to have suffered as much damage as Tokyo in the 1954 appearance of Godzilla, or anywhere near the loss of human life. As more dai kaiju attacks took place, the Japanese government agency concerned with civil defense got much better at getting the civilians out of harm's way, so the number of casualties continually dropped. This made the attacks easier for the population to deal with the periodic appearances as the damage became more in line with what you would expect from a strong earthquake, tsunami, typhoons, tornadoes, hurricanes, and the like---mostly economic damage, with relatively few lives lost. However, Tokyo was all but completely destroyed in the 1954 visit by Godzilla. By 1961, seven years later, it has been completely rebuilt, and with a lot of new designs and construction materials for the buildings. Tokyo looks relatively shiny because of all of the new construction, and because most of the old buildings had been razed by either Godzilla or construction crews.

At this point in time, the US was helping to fund the rebuilding of Japan after World War II with an equivalent to the Marshall Plan being used to rebuild Europe. However, Japan's economic miracle had not yet started, so their economy was still in depression, or at least a deep recession (like America in the 1970's). Japan would probably not have been able to fund the rebuilding of Tokyo, and was too far in debt to afford it. While America was in a position to both rescind the previous debt structure and issue new loans, or to simply ignore the credit rating of Japan and issue new loans, that would probably have been a bad idea to the conservative administration of Dwight D. Eisenhower. (or in the timelines where Patton became president.) The inflation generated by this would have probably kept Japan crippled for decades, and they never would have been able to afford the later, smaller rebuildings. Yet we see not only shiny rebuilt cities in Tokyo and Osaka, but we see much evidence of advanced scientific research, which is fairly obviously funded by Japan, not the world (the big Markelite, or maser, cannons would have been built in Japan, not shipped over from America; also see the science facility at Solgell Island, which is trying to learn how to control the weather---definitely Japanese funded).
However, it would have been far simpler for the big Japanese businesses to issue new stock in the US, Canada, Australia, New Zealand, and Britain to raise quick capital for construction of new buildings. The influx of hard cash was able to bring in lots of construction crews--both domestic workers from other Japanese cities, as well as jobless refugees from Tokyo, plus foreign work crews (probably mostly American, as we had a lot of construction workers in the US since World War II). The workers would, of course, spend much of their cash in Japan, and the multiplier effect took off at warp speed. In about the same amount of time that the US and Japan were engaged in hostilities, the Japanese-American economic alliance had managed to rebuild Tokyo and Osaka into shining examples of the new pleasant Trans-Pacific relationship. The economic boom found itself rebuilding the later dai kaiju rampages almost effortlessly. Leftover technology from the alien invasions (especially from the Mysterians) led to a strong boost in science, which enabled a corresponding increase in space technology, maser weaponry, the psionic amplifier seen in Godzilla's Revenge, and the weather control research base on Solgell Island--all within about 20 years of Godzilla's first appearance. Forcefield technology, more advanced spacecraft, and more powerful weaponry appeared in the next 15 years, and by the middle of the 21st century, humankind was all over the solar system, with significant bases on the Moon, on Mars, and various asteroids and moons elsewhere in the outer part of the solar system.
The basis for this, the partnership between America and Japan, saw a tremendous swing from occupier/occupied to a genuine friendship rivaled by our own timeline's US-UK friendship before the year 2000. The middle classes of both the US and Japan saw a great deal of return on their stock investments, and in the best Japanese tradition, the returns kept getting re-invested (instead of being wasted on consumer goods, as in our timeline). (One disastrous and unintended side effect was increased industrial output, leading to more pollution, and the creation of Hedorah, the Smog Monster in 1971.)
After the major work rebuilding Tokyo was completed, many Americans stayed in Japan, intermarrying into the local populace, and strengthening the ties between the former foes. Others came home and helped build a strong national rail infrastructure, echoing the building of the bullet train system in Japan. (Necessary in Japan due to heavy population concentration in the cities, this bypassed the massive freeway construction in the US in our timeline; this allowed more of our resources to go into the space program.) One person who came to Japan and stayed was not a construction worker, but instead a former Marine fighter pilot turned astronaut. His name: John Glenn. We do not know what happened to him after he lost his fiancée, Miss Namikawa, during the second visit of King Ghidorah. We do not know if he stayed in Japan, stayed in the space program, or returned to the US and became a senator from Ohio.

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