Short answers, pulled from the story.
Japanese naval codes were the cryptosystems used by the Imperial Japanese Navy to protect its communications during World War II. Every code the IJN used was eventually broken by Allied codebreakers, enabling operations such as the American victory at the Battle of Midway in 1942 and the shooting down of Admiral Isoroku Yamamoto in 1943.
JN-25 was the main, most secure communications code used by the Imperial Japanese Navy, introduced on the 1st of June 1939. It required reconstructing thirty thousand code groups and thirty thousand random additives. John Tiltman, with some assistance from Alan Turing at the Government Communications Security Bureau, had broken JN-25 by 1941; a key structural clue was that every number in the codebook was divisible by three.
Exploitation of JN-20, an inter-island cipher, produced the intercept that the target designated "AF" was short of water, confirming Midway Island as the main Japanese fleet objective. Separately, JN-25b, the version in use at the time, had been broken enough to reveal Japanese attack plans, allowing the U.S. Navy to prepare an ambush.
Agnes Driscoll broke the additive portion of the Red Book code after three years of work following its capture in 1923. John Tiltman, with help from Alan Turing, broke JN-25 by 1941. Commander Joseph Rochefort commanded Station HYPO at Pearl Harbor. John MacInnes and Brian Townend at the British FECB in Kilindini cracked JN-40 in late 1942.
In June 1942 the Chicago Tribune published an article implying the United States had broken Japanese codes and knew in advance about the Midway attack. Commander Morton T. Seligman had shown Nimitz's executive order to reporter Stanley Johnston. Despite the exposure, the Japanese concluded the Allies had used traffic analysis or captured codebooks rather than broken the codes, so they did not overhaul their cryptographic systems.
On the 28th of May 1941 U.S. Customs Service Agent George Muller and Commander R. P. McCullough boarded the Japanese whale factory ship Nisshin Maru No. 2 in San Francisco and seized her codebooks. Copies were made and the originals returned, but the operation was clumsy enough that the Japanese quickly realized JN-39 was compromised and replaced it with JN-40.