Admiral Nimitz had one critical advantage: US cryptanalysts had partially broken the Japanese Navy's JN-25b code.[51] Since early 1942, the US had been decoding messages stating that there would soon be an operation at objective "AF". It was initially not known where "AF" was, but Commander Joseph Rochefort and his team at Station HYPO were able to confirm that it was Midway: Captain Wilfred Holmes devised a ruse of telling the base at Midway (by secure undersea cable) to broadcast an uncoded radio message stating that Midway's water purification system had broken down.[52] Within 24 hours, the code breakers picked up a Japanese message that "AF was short on water".[53] No Japanese radio operators who intercepted the message seemed concerned that the Americans were broadcasting uncoded that a major naval installation close to the Japanese threat ring was having a water shortage, which could have tipped off Japanese intelligence officers that it was a deliberate attempt at deception.[54]

HYPO was also able to determine the date of the attack as either 4 or 5 June, and to provide Nimitz with a complete IJN order of battle.[55]

Japan had a new codebook, but its introduction had been delayed, enabling HYPO to read messages for several crucial days; the new code, which took several days to be cracked, came into use on 24 May, but the important breaks had already been made.[56]

As a result, the Americans entered the battle with a good picture of where, when, and in what strength the Japanese would appear. Nimitz knew that the Japanese had negated their numerical advantage by dividing their ships into four separate task groups, too widely separated to be able to support each other.[57] This dispersal resulted in few fast ships being available to escort the Carrier Striking Force, reducing the number of anti-aircraft guns protecting the carriers. Nimitz calculated that the aircraft on his three carriers, plus those on Midway Island, gave the U.S. rough parity with Yamamoto's four carriers, mainly because American carrier air groups were larger than Japanese ones. The Japanese, by contrast, remained mainly unaware of their opponent's true strength and dispositions even after the battle began.

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