Of all captains in the history of the United States Navy, he is the only one subjected to court-martial for losing a ship sunk by an act of war, despite the fact that he was on a top secret mission maintaining radio silence.

Following years of efforts by some survivors and others to clear his name, McVay was posthumously exonerated by the 106th United States Congress and President Bill Clinton on October 30, 2000.

Later that year, Indianapolis received orders to carry parts and nuclear material to Tinian to be used in the atomic bombs which were soon to be dropped on Hiroshima and Nagasaki.

About 300 of the 1,196 men on board either died in the initial attack or were trapped belowdecks and drowned when compartments were sealed to prevent sinking.

[6] After a Navy Court of Inquiry recommended that McVay be court-martialed for the loss of Indianapolis, Admiral Chester Nimitz disagreed and instead issued the captain a letter of reprimand.

Admiral Ernest King overturned Nimitz's decision and recommended a court-martial, which Secretary of the Navy James Forrestal later convened.

However, in 1946, at the behest of Admiral Nimitz who had become Chief of Naval Operations, Secretary of the Navy Forrestal remitted McVay's sentence and restored him to duty.

[7][8] Hashimoto, the Japanese submarine commander, was on record as describing visibility at the time as fair, which is corroborated by the fact that he was able to target and sink Indianapolis in the first place.

An additional point of controversy is evidence that the admirals in the United States Navy held some responsibility for placing the ship in harm's way.

On July 24, 1945, just six days prior to the sinking of Indianapolis, the destroyer Underhill was attacked and sunk in the area by Japanese submarines, yet McVay was never informed of this event, and several others, in part due to issues of classified intelligence.

[13][14] In his book Abandon Ship, author Richard F. Newcomb posits a motive for Admiral King's ordering McVay's court-martial.

[17] This is also untrue, as police reports obtained by the Legacy Organization do not mention this nor show any other objects in the pictures aside from his pistol.

[19] McVay also struggled throughout his life from the impact of vitriolic letters and phone calls he periodically received from grief-stricken relatives of dead crewmen who served aboard Indianapolis.

Paul Murphy, president of the USS Indianapolis Survivors Organization, said: "Captain McVay's court-martial was simply to divert attention from the terrible loss of life caused by procedural mistakes which never alerted anyone that we were missing."

Over fifty years after the incident, a 12-year-old student in Pensacola, Florida, Hunter Scott, was instrumental in raising awareness of the miscarriage of justice carried out at the captain's court-martial.

As part of a school project for the National History Day program, the young man interviewed nearly 150 survivors of the Indianapolis sinking and reviewed 800 documents.