In 1290 Margaret the Maid of Norway, sailed from Norway to Scotland to be crowned Queen, and to eventually marry Prince Edward, the future King of England, thus uniting the two realms. But they stopped in the Orkney Islands after rough weather, and Margaret died, allegedly of sea sickness, and there were 300 more years of on and off wars between England and Scotland, and thousands of people died.
It is true that it is possible to die from sea sickness, and Margaret was only 7 years old, but it still seems a bit strange and maybe Margaret had other conditions. Or maybe a Kaiju rose from the sea by the ship, and terrified Margaret half to death, and then breathed poisonous vapors on the ship, weakening everyone and contributing to Margaret's death.
Mansa Musa (reigned 1312-37) of the Malian Empire made a famous pilgrimage to Mecca in 1324-26. In Cairo Musa is said to have told of the fate of his predecessor Abu Bekr II:
The ruler who preceded me did not believe that it was impossible to reach the extremity of the ocean that encircles the earth (meaning Atlantic), and wanted to reach that (end) and obstinately persisted in the design. So he equipped two hundred boats full of men, as many others full of gold, water and victuals sufficient enough for several years. He ordered the chief (admiral) not to return until they had reached the extremity of the ocean, or if they had exhausted the provisions and the water. They set out. Their absence extended over a long period, and, at last, only one boat returned. On our questioning, the captain said: 'Prince, we have navigated for a long time, until we saw in the midst of the ocean as if a big river was flowing violently. My boat was the last one; others were ahead of me. As soon as any of them reached this place, it drowned in the whirlpool and never came out. I sailed backwards to escape this current.' But the Sultan would not believe him. He ordered two thousand boats to be equipped for him and for his men, and one thousand more for water and victuals. Then he conferred on me the regency during his absence, and departed with his men on the ocean trip, never to return nor to give a sign of life.1
https://en.wikipedia.org/wiki/Abu_Bakr_II2
And maybe a kaiju was responsible for the non return of the Malian fleet.
In Greek mythology Cassiopea, Queen of Aethiopia, boasted that her daughter Andromeda was more beautiful than the Nereids, angering Poseidon, God of the Sea, who sent a sea monster, Cetus, to ravage the coasts. King Cepheus chained Andromeda to a rock to placate Cetus, but Perseus killed Cetus and saved Andromeda.
And possibly Cetus was a kaiju.
According to Procopius History of the Wars VIII, xxix
It was at that time also that the whale, which
the Byzantines called Porphyrius, was caught. This
whale had been annoying Byzantium and the
towns about it for fifty years, not continuously, how-
ever, but disappearing sometimes for a rather long
interval. And it sank many boats and terrified the
passengers of many others, driving them from their
course and carrying them off to great distances. It
had consequently become a matter of concern to the
Emperor Justinian to capture this creature, but he
was unable by any device to accomplish his purpose.
But I shall explain how it came to be captured in
the present instance. It happened that while a deep
calm prevailed over the sea, a very large number of
dolphins gathered close to the mouth of the Euxine
Sea. And suddenly they saw the whale and fled
wherever each one could, but the most of them
came in near the mouth oi the Sangarius. Mean-
while the whale succeeded in capturing some of
them, which he swallowed forthwith. And then,
either still impelled by hunger or by a contentious
spirit, it continued the pursuit no less than before,
until, without noticing it, it had itself come very
close to the land. There it ran upon some very deep
mud, and, though it struggled and exerted itself to
the utmost to get out of it as quickly as possible, it
still was utterly unable to escape from this shoal, but
sank still deeper in the mud. Now when this was
reported among all the people who dwelt round
about, they straightway rushed upon the whale, and
though they hacked at it most persistently with
axes on all sides, even so they did not kill it, but
they dragged it up with some heavy ropes. And
they placed it on waggons and found its length to
be about thirty cubits, and its breadth ten.^ Then^
after forming several groups and dividing it accord-
^ About 45 feet by 15 feet.
ingly, some ate the flesh immediately, while others
decided to cure the portion which fell to them.
Now the Byzantines, observing the earthquakes
and learning the circumstances of the Nile's rise and
the capture of this whale, began straightway to
prophesy that such and such things would take
place, according to the taste of each. For men are
wont, when present events baffle them, to utter awe-
some prophecies of the future, and, distracted by
occurrences which trouble them, to infer, with no
good reason, what the future will bring forth.
But as for me, I shall leave to others prophecies and
explanations of marvels ; still, I know well that the
lingering of the Nile on the fields did prove a cause
of great calamities at that time at any rate, while
the disappearance of the whale, on the other hand,
unquestionably provided an escape from many
troubles. However, some say that it was not the
same whale that I mentioned, but another one that
was captured. But I shall return to the point where
I made the digression from my narrative.
https://archive.org/stream/procopiuswitheng04procuoft/procopiuswitheng04procuoft_djvu.txt3
So the ship-sinking Porphyrius (or possibly another creature mistaken for him) was killed about the time of earthquakes and severe Nile Floods and famines. This seems to be fairly shortly before Empress Theodora died in 548 AD. And perhaps the ship-sinking Porphyrius was a Kaiju.
And maybe the giant "serpent" that fought the army of Regulus in 256/255 BC was a some kind of Kaiju.
https://www.ancientworldmagazine.com/articles/regulus-bagradas-dragon/ 4
Anyway, these are a few ideas I thought of.
Added 10-13-2018.
The army of Regulus mentioned above was later defeated by the Cartharginians and thousands of Roman soldiers were killed or captured. This Roman defeat was thus a significant event for thousands of Romans and their families. And I am not familiar with what the ancient sources said about the defeat of the Roman army.
But maybe some Roman sources claim the carthaginians didn't defeat the Romans easily. If defeat or victory balanced on a knife's edge, possibly the earlier battle with the giant serpent was enough to tip the scales against the Romans. If no ancient sources claimed that, one could always invent a newly discovered account which does claim that Regulus's army would have defeated the Carthaginians if not for the earlier fight with the giant serpent.
I have thought that kaiju could be responsible for the disappearance of some exploring expedition. For example, there was the Franklin expedition to the Arctic to find the northwest Passage in 1845-1848. Of course you can't just say that a giant kaiju smashed the ships to splinters. Both have been found well preserved in ice cold waters in recent years, and a note explaining they had been trapped in the ice and abandoned was found 150 years ago.
But three sailors were buried on the island where the expedition spend the first winter, and the note specified how many more had died before abandoning the ships trapped in the ice. And of the specified remaining crew who left on a death march toward safety hundreds of miles away in Canada, the skeletons of many have been found, but many other skeletons and graves remain undiscovered.
It certainly would be possible to write a story in which some unaccounted for crew members could have been the victims of a kaiju.
But there was a recent TV series The Terror (2018-?) whose first season involved some sort of terror stalking the crews of the icebound HMS Erebus and HMS terror.
In 1848 Dr. Ludwig Leichhardt and six companions set out on his third exploring expedition, an attempt to cross Australia from east to west, and the expedition was never heard of again except for possible relics, aboriginal rumors, and various scattered clues. So it would be possible to write a story in which some Australian bunyip, really a form of kaiju, was responsible for the disappearance.
According to the Bible, Sodom and Gemorrah were destroyed by fire and brimstone from the sky, obviously the wrath of God. Or maybe a volcanic eruption? Or perhaps the flaming breath of some dragon-like kaiju?
Similarly the Historia Brittonum claimed that the fifth century British monarch Vortigern was burned down in a a wooden fort with his people by fire from heaven. Or maybe it was fire from a dragon-like Kaiju.
Another British monarch, Maelgwn Gwynedd, died about a century later, allegedly about 547, 548, or 549. According to one story he died during the "yellow plague". But maybe not of the "yellow plague", because one story has him fleeing to the church at Rhos and locking himself in for safety. But he looked out the keyhole and saw the "yellow plague" and died, possibly from fright. And possibly he saw some horrifying kaiju.
Then there was the story of the sinking of the schooner Pearl by some giant squid or octopus in 1874.
http://www.sundaytimes.lk/991212/plus5.html5
A ship-sinking chepalopod that sinks a ship is definately kaiju-like.
In the 1490 Ch'ing-yang events, many stones allegedly fell from the sky on the city. Some sources say that 10,000 people were killed. Was this the deadliest meteor shower in history, or the deadliest hailstorm, or something caused by a a Kaiju?
https://en.wikipedia.org/wiki/1490_Ch%27ing-yang_event6
In the 1760s the Beast of Gevauden killed a number of people in France. It is usually said to have been one or two man-eating wolves, but more exotic explanations have been made, so maybe it was some baby kaiju.
Then there was the legendary Great White Whale, Mocha Dick, a partial inspiration for you-know-who. Mocha Dick smashed a number of whale boats, but I don't know if Mocha Dick ever sank any whale ships like some other whales did. But a number of sources on the internet claim that Mocha Dick sank a varying number of whaling ships.
This article claims that Mocha Dick sank over 20 whaling ships.
http://www.todayifoundout.com/index.php/2011/12/a-real-life-white-whale-that-destroyed-over-20-whaling-ships-and-survived-encounters-with-another-80/1
And I have read a claim that remains of a number of whaling ships were found in the waters near Mocha Island. So possibly there could be a story in which Mocha Dick was not a Physeter macrocephalus but some sort of kaiju.
Added 10-14-2018 There is the story that Cambyses II (r.530-522 BC) "The great king, the king of kings, the king of lands and people, the king of the world" conquered Egypt and then sent an army of 50,000 men to conquer the Oasis of Ammon or Siwa and they were wiped out by a giant sandstorm in the desert. Or maybe by a kaiju.
Here are mentions of several shipwrecks where important people died.
https://history.stackexchange.com/questions/40071/apart-from-the-white-ship-in-1120-have-there-been-any-other-maritime-disasters/47957#479577
And possibly some of those deaths could have been caused by Kaiju.
The Great Dam of Ma'rib in Yemen was built, repaired, and rebuilt over centuries and possibly millennia, the first inscription there is dated to 760 to 740 BC. It was used to provide irrigation for crops to support many thousands of people. There were breeches in the dam in 145 BC, and in AD 449, 450, 542, and 548. After the final breech and flood in 570-575 the dam was not repaired and tens of thousands of people left to seek other homes. And possibly the dam was busted by a Kaiju.
The Kyshtym disaster in 1857 is considered the third worst nuclear disaster. Inadequate storage of nuclear waste led to an explosion and the release of radioactive waste of the a wide area and the evacuation of about 10,000 people from from an area of hundreds of square miles and an unknown number of cases of cancer. And even though the causes are well known, to most people the disaster is just a vague rumor and so the idea of it being caused by a Kaiju may seem fairly plausible.
https://en.wikipedia.org/wiki/Kyshtym_disaster8