Were U.S. ships attacked in Tokyo Bay?

For what this might be worth, this is a list of USMC personnel who died between 30 August 1945 and 4 September 1945. Name, service number, and, at least, where they were at the time of death. It does not appear that any of these deaths occurred in Japan or the waters around Japan. Names can be found here searching by date and the information is from the USMC Casualty Cards (that’s what the “(mc)” denotes) which if you’ve access to Fold3 can be found transcribed here.

• BOND, Robert Owen Joseph, 528394, CasCo1, MarBks, NOB, Terminal Island, San Pedro, Calif, August 30, 1945, died of wounds (mc)

• PENA, Louis Raymond, 439927, HqCo, 2ndBn, 25thMar, 4thMarDiv, FMF, August 30, 1945, accidental death (mc)

• SHAFFO, Joseph Clement, 529596, H&SCo1, 3rdMar, 5thMarDiv, FMF, August 30, 1945, accidental death (mc)

• KOTOUKIS, George Nicholas, 948444, CasCo2, MarBks, NOB, Terminal Island, San Pedro, Calif, August 31, 1945, died (mc)

• POWROZNIK, Chester Edward, 555395, CasCo, RecDep, MarBks, Parris Island, SC, September 1, 1945, died (mc)

• JAHN, Vernon Bernard, 959760, CoA, 1stBn, 4thMar, 6thMarDiv, FMF, September 2, 1945, accidental death (mc)

• LIBBEY, Herbert Lee, 29531, VMF-225, MASG-51, MFAWC, MCAS, Santa Barbara Calif, September 2, 1945, died (mc)

• MACDONALD, Francis Xavier, 170931, BksDet, MarBks, NYD, Boston, Mass, September 2, 1945, died (mc)

• STRADLEY, Francis Robert, 887080, Co, NRC, NT&DC, Farragut, Idaho, September 2, 1945, accidental death (mc)

• BRANHAM, Parish Loving, 960098, EC, R&RC, MarBks, NYd, Philadelphia, Pa, September 3, 1945, accidental death (mc)

• FRAZIER, Richard Don, 316022, HqSqn, MCAD, Miramar, San Diego, Calif, September 3, 1945, died (mc)

• GERDING, Lester Joseph, 486547, CoF, 2ndBn, 2ndMar, 2ndMarDiv, FMF, September 3, 1945, accidental death (mc)

• GRANLEE, Harry Bertram, Jr, 491031, CoC, 1stArmdAmphBn, FMF, September 3, 1945, accidental death (mc)

• RITTER, Harvey Paul, 462030, GdDet, MarBks, NATB, Pensacola, Fl, September 3, 1945, accidental death (mc)

• CASE, George Able, 446682, MarBks, NAD, Fallbrook, Calif, September 4, 1945, accidental death (mc)

• MORROW, Claude Levern, 305012, 1stGdCo, GdBn, MT&RC, Camp Pendleton, Oceanside, Calif, September 4, 1945, accidental death (mc)

• NEAR, Ray William, 12756, HqCo, MCB, NOB, Guantanamo Bay, Cuba, September 4, 1945, died (mc)

I find these list to be fairly accurate, they even include those who died in hospital care which the Navy loss list I have does not, although with naval aviators I tend to have more information on the loss in my records, especially when someone is noted as being assigned to “POW&MPDet, HQUSMC, Washington DC”. After someone has been missing for 30 days without prospect of recovery they were transferred from whatever unit/squadron to the Prisoner of War and Missing Personnel Detachment . . . strictly a paperwork legal formality on the way to being declared dead.

All of the Marines on this list were enlisted men except for LIBBEY, Herbert Lee, who was a 1st Lieutenant at the time of his death and NEAR, Ray William, who was a Major at the time of his death.

Verify:

My father was a radar technician on a U.S. destroyer and since he was a "College Boy" math major he was sent over to join the prize crew on a Japanese ship (I think the Nagato) His assignment was to check out the ship's electronics and to write a report on what he found.

The Nagato was a Battleship. It was Yamato's flagship for the attack on Perl Harbor.

Nagato Class Battleship see Nagato

Admiral Isoroku Yamamoto issued the code phrase "Niitaka yama nobore" (Climb Mount Niitaka) on 2 December 1941 from Nagato at anchor at Hashirajima to signal the 1st Air Fleet (Kido Butai) to proceed with its attack on Pearl Harbor.

First was the Battleship Nagato damaged? was it at Tokyo Bay Sept 1945? and were Americans in possession of that ship prior to the former surrender Sept 2, 1945? The answer to these questions are YES.

The Nagato was an older Battleship being used as an air defense platform later in the war. The above Link says on August 30th 1945 US sailors took control of Nagato a few days before the formal surrender, after it was struck by 2 bombs which killed 30 Japanese Sailors.

This link shows a picture of the Nagato in Tokyo Bay Sept 3, 1945 days after the U.S. sailors took control and one day after the formal Japanese surrender on Sept 2, 1945.

Conclusion:
If your father was in Tokyo Bay late August of 1945 it is possible he was on the Nagato.

Verify:

He said that one night while he was on this Japanese ship a group of Japanese fanatics climbed the anchor chain and killed the lookout on the bow. They were then all killed by the marines on the prize crew. Apparently several attackers, stumbling around in the dark, also fell through bomb holes in the deck and drowned in the ships fuel oil tanks.

Probable not? The last American death of WWII in the Pacific is given Aug 18, 1945 nearly two weeks prior to the US taking possession of the Nagato and two days after the Emperor's surrender. U.S. Army Sargent Anthony Marchione

However, As late as mid August 1945, there were attempt by renegades in the Japanese Military to take control of the Emperor and continue the war. They actually came pretty close to stopping the Emperor's surrender radio address to the Japanese people. See Hatanaka's rebels Aug 12-15th 1945. Also there were Japanese soldiers who had never accepted the surrender still turning up decades after the war. Japanese Holdouts. Suffice it to say there were a lot of Japanese military unhappy with the surrender in August of 1945 and those loyal to the Emperors wishes gave a lot of thought to them throughout the negotiations.

Tony Tully, co-author of Shattered Sword, penned a short history of Nagato’s last year in IJN service and beyond to Operation Crossroads found here. Makes no mention of any assault on the ship and even notes that the Japanese crew were still aboard AFTER the USN had taken possession which occurred on 30 August, but three days before the actual surrender, not to mention the ordnance still aboard including a small cache of firearms. Tony is usually pretty thorough.

For what it is worth, I have in my possession an IJN commodore’s pennant from Nagato’s signal bridge and a brass switch cover, both collected after the surrender by then Commander Noel Gayler of the TF38 staff and given to my father with whom he worked in the TF operations staff. Their boss, Captain John “Jimmie” Thach can be clearly seen in most photos showing allied officer witnesses.

One might also note that US forces were already ashore at Yokosuka by 30 August. Not many, but they were there and there were no incidents with holdouts.

Perhaps you are thinking of something else; there were no attacks on the ships gathered in Tokyo Bay for the Japanese surrender. Not that no one was unprepared, they were very prepared, just nothing happened.

Boarding and fighting it out on deck was pretty rare in WW2, I can think of but two, though I am sure there were others, in the Pacific

Sinking of the Japanese submarine I-1

And right at the end two USN operated Junks taking on a Japanese Junk after they were fired on.

I can't find any support for it online either.

However, such a thing would have been entirely within character for the Japanese military of the time, which was extreme ultranationalist. Honestly, we almost need another new superlative beyond "ultra" there. They should be the yardstick by which any other "ultranationalist" contenders are measured. Particularly in the junior officer corps, which was inclined toward taking spontaneous violent action both against both external and internal political enemies. Many historians have termed their form of government in the runup to the war as government by assassination.

The Japanese leadership, knowing how their society worked, fully expected an anti-surrender coup attempt after the decision to surrender was made, and in fact one happened. The conspirators managed to murder the head of the Imperial Guard and take over the palace. However, they never managed to find where the Emperor was holed up. Their political assassination squad also missed the Prime Minister, only managing to burn his office and house down. About an hour after the coup attempt ended, the Emperor publicly announced Japan's surrender.

There were in fact some organized air attacks on American B-32's overflying Tokyo about a week later. After the second one, further such attacks were prevented by removing the propellers from the Japanese interceptors.

Among those most capable of translating those feelings into action were the Japanese navy fighter pilots at Atsugi and Yokosuka airfields, outside Tokyo. At Atsugi, the 302nd Air Group was openly rebelling against Hirohito’s cease-fire order. And the Yokosuka Air Group included many pilots—such as aces Saburo Sakai and Sadamu Komachi—who felt Japan’s airspace should remain inviolate until a formal surrender document had actually been signed.

If pilots felt that way about aircraft over Tokyo airspace, it doesn't seem like much of a leap for some in the Army to have also felt that way about ships in Tokyo harbor.

It would have also been within their capabilities. There was a group of Japanese frogmen being trained to carry out suicide attacks on US ships using stick mines. 1200 soldiers were trained up, and it appears the only thing preventing the plan from going into action was the fact that the stick mines couldn't be made ready in time. Additionally, there were swimmer attacks earlier in the year in Palau, although using explosives (like the frogmen were being trained for), rather than boarding. But the fact remains that there were military frogmen trained to attack the invader's ships in harbor at the time of surrender.

It also seems possible such an incident may have gone relatively unheralded. Before I started researching this question, I'd never heard of the post-surrender air attack incidents. It looks like we only know about them now because author Stephen Harding interviewed the US airmen involved back in the 1990's while researching a book.

So your remembered story seems entirely plausible, both in time and place. However, without a primary source attesting to it, is probably going to have to remain in the realm of legend.