This scenario appeared on Today in Alternate History with further thoughts on my end. 
"The  [Battle of Midway was] the most stunning and decisive blow in the history of naval warfare" ~ military historian John KeeganOn this day in alternate history Fleet Radio Unit Pacific (a.k.a. Station HYPO) was destroyed by a stray Japanese bomb that exploded in the basement of the Old Administration Building at Pearl Harbor. 
Aside
 from another human tragedy on the "day of infamy" it was another 
set-back to the Allies in the Far East because the late Commander Joseph
 Rochefort had assembled a team of the U.S. Navy's best 
cryptanalysts. However, despite their potential for changing the course 
of the Pacific War, they had actually made little progress to date in the
 decryption of the Imperial Japanese Navy's most secure cypher systems. 
In LCDR Rochefort's last report to OP-20-G Naval Intelligence section in
 Washington, he estimated that less than 10 percent of traffic had been 
decrypted. Fatefully, this report was sent before a new system was 
introduced on the eve of the attack on Pearl Harbor.
Of course, 
losing the ability to read Japanese coded messages was quite a 
blow, but not a fatal one, to the Allied cause. After all, the Japanese 
were already over-extended, and the US just had too many resources for 
Japan to conquer it.
Moreover, naval radio intelligence centers in Australia, Ceylon, and 
later Kenya would continue the work of Station HYPO. 
The lack of really meaningful progress was highlighted by a
 second surprise attack on Midway Atoll in which all three US Yorktown 
class carriers were sunk. This outcome gave Tokyo complete control over 
the Solomon Islands and Port Moresby. The supply lines between the 
USA/Panama and Australia would be interrupted, but, despite Allied fears, 
Australia itself would not fall. Still, the decisive battle of the 
Pacific War would be fought in the Gilbert Islands nearly eighteen long 
months after Pearl Harbor when the Essex-class fleet carriers and 
Independence-class light carriers had become available.
Terror of Japanese raids on the western coast of America spurred monumental naval construction with citizens rallying to fund war bonds and donate scrap metal. While the US Navy struggled to rebuild its ships, the Marines redoubled efforts to strengthen the hold on Aleutian Islands. Vicious island-hopping campaigns pushed forward every summer until a strong link had been built to allied USSR Kamchatka, where Americans began assembling for a push across the Sea of Okhotsk toward the sparsely populated northern Japanese islands. Near-constant air-battles raged from land bases on either side, which wore down the Japanese air force that did not have as expansive resources as the Allies to recover from losses. With Allied naval fleets pushing northward from the re-taken Philippines and air fleets pushing from the south to dominate with air superiority, Japan was caught in a devastating pincer that prompted defeat.
At the same time, President Roosevelt and British Prime Minister Winston Churchill were finalizing the Quebec Agreement
 under which the US and UK would pool their resources in order to 
accelerate the development of nuclear weapons. The merging the British Tube Alloys project with the American Manhattan Project
 would create a Combined Policy Committee to control the joint project. 
Of course by the time of the successful Trinity Test, the outcome of the 
Pacific War had been long settled. Yet the availability of nuclear 
weapons provided the opportunity to dramatically shorten the remainder 
of the conflict, and what is more, to reduce the need for Soviet 
intervention in the Far East. 
However, the logistical constraint was 
that the atomic bomb was simply not deliverable by bomber due to the 
lack of range of the B-29 from the nearest Allied airbase and because 
the B-29 could not be launched from the Essex-class carriers. In reality, the 
conclusion of the war was predicated upon the occupation of Okinawa. By this stage, Roosevelt was already dead, and his successor, 
Harry Truman, was far less accommodating to the interests of the Soviet 
Union. The combination of these factors would draw the Pacific War out 
into 1946 by which time the US had sufficient stockpile of nuclear 
weapons to force the outcome on their own terms.
Wikipedia Note: the work of Station HYPO allowed Admiral Nimitz to gamble on the ambush
 that resulted in the Battle of Midway, the loss of four Japanese 
carriers and many naval aviators for much lower Allied losses, and what 
is generally agreed to have been the turning point of the Pacific War. 
Nevertheless, the precise importance and role of HYPO in penetrating the 
Japanese naval codes has been the subject of considerable controversy, 
reflecting internal tensions amongst US Navy cryptographic stations. 
