One of the most violent escape attempts on Alcatraz occurred in May of 1946. Many historians mark this date as the most significant event in the island's twenty-nine-year history as a Federal penitentiary, and it was appropriately christened the "Battle of Alcatraz." In the wake of the conflict, fourteen guards and one inmate were left injured, while two correctional officers and three inmates lay dead from bullet wounds. A bank robber from Kentucky named Bernard Paul Coy, who was serving out a twenty-six-year sentence on The Rock for committing a holdup using a sawed-off shotgun, devised a forceful escape strategy with five accomplices. Coy had carefully studied the habits of various guards over a period of several months. Then on May 2, 1946, aided by accomplice Joseph Cretzer, Coy smeared axle grease over his chest, head, and extremities, and started climbing the West End Gun Gallery from the juncture at Times Square and Michigan Avenue. Climbing hand over hand, he scaled the barred cage until he reached the top. Clenched in his teeth was a small cloth bag containing a crudely fashioned bar-spreader device that had been fashioned from toilet fixtures in one of the prison workshops. Coy set the device firmly between two bars (which were approximately 5 inches apart), and using a small wrench, he was able to exert enough force to effectively spread the bars and create an opening nearly ten inches in width. It is believed that Coy had also been limiting his intake of food in order to reduce his body mass. With Crezter eagerly watching his progress from below, Coy painfully squeezed his body through the opening, and made his entrance into the West Gun Gallery.

Coy quickly secured a riot club and positioned himself in a low crouch, so that the officer on duty couldn't see him when looking through the door's access window. Waiting in ambush, his accomplices lured the officer out. As the unsuspecting guard passed through the doorway, Coy forcefully hurled the steel door forward, throwing the officer off balance, and brutally clubbed him, forcing him to the floor. He then strangled him into unconsciousness with his necktie. Working swiftly, Coy lowered firearms and riot clubs to his partners below, and searched for keys that would provide access to the recreation yard. The convicts were now fully armed, and were able to capture nine unarmed guards and lock them into cells #404 and #403, located at the juncture of Seedy Street and Times Square. But their escape plan soon began to crumble, as they were unable to locate the key that would unlock the door leading to the recreation yard. The key had been concealed by a brave correctional officer named Miller, who had surrendered all of his keys to the convicts except the most critical one. Miller had been able to quietly hide the key in the toilet of the cell where he and the other correctional officers were being held hostage. Meanwhile, Coy & Cretzer had released three other accomplices from their cells. Clarence Carnes (the youngest convict ever sent to Alcatraz), Sam Shockley, and Miran Thompson were all serving sentences for violent crimes. When the breakout was discovered the distress sirens of Alcatraz wailed, indicating grave trouble at the prison, and the sound could easily be heard from the shores of San Francisco. The Coast Guard and the Marines were mobilized to furnish the support of demolition and weapon experts, and all the off-duty correctional officers were brought in to help take back the cellhouse from the armed and desperate convicts.

Since the takeover had occurred after lunch, the majority of the prison inmates were in the Industries, and the cellblock was largely empty. Marines assisted correctional officers in assembling all of the industry workers into the recreation yard, and helped to gather blankets and jackets for the inmates who were unable to return to their cells. Meanwhile inside the cellblock, a battle was raging. The escapees, realizing that they were unable to gain access to the recreation yard, had become desperate. In a violent rage, and cheered on by inmates Shockley and Thompson, Joseph Cretzer took his revolver, and leaning against the bars of cell #403, started unloading rounds into the cramped cell. Officers fell in the hail of gunfire, some critically wounded. Back at the Administration Office the Warden had called together his lieutenants, and they had formulated a plan to send in strike teams to rescue the guards who were being held captive. Lt. Phil Bergen was assigned to lead the first team into the cellhouse through the West End Gun Gallery. As the team approached, two guards first fired several rounds to clear the corridor. The team then rapidly made their entry into the Gallery, and mounted the stairs to the first level. As one of the inmates fired rifle rounds at the assault team, Bergen worked feverishly to rescue the officer who had been ambushed by Coy.

Harold Stites was one member of Bergen's team who courageously returned fire, attempting to suppress the convicts' barrage. Stites was no stranger to this type of scenario. In 1938, three inmates had rushed him while he was on post in a guard tower. In an attempt to stop them from securing firearms, he was forced to shoot two inmates, one of them fatally. The 1938 escape attempt was one of the most violent in the island's history, and resulted in the death of a correctional officer, who was fatally assaulted with a hammer by inmate named Rufus Franklin. As Bergen provided medical care to the downed officer, Stites continued to spray rifle fire into the cellhouse. Then suddenly Stites was struck by a bullet, and yelled out that he'd been hit. Three other officers were also hit by gunfire during this assault. Stites was carried unconscious out of the Gun Gallery and laid onto a couch. He was quickly examined by the prison's physician, and pronounced dead. Stites would be the first casualty of the "Battle of Alcatraz." The other officers were quickly transported by boat back to the mainland, to be taken by ambulance to a local hospital. Bergen and four other officers returned to the Gun Gallery, and communicated with the prison staff via one of the Gallery phone lines. It appeared that an inmate was running from cell to cell firing random shots into the Gallery. At a little after 10:00 p.m., the Associate Warden took a group of fourteen officers and burst into the cellhouse, hoping to rescue their colleagues. The team fell under heavy gunfire from the inmates who had positioned themselves on top of C Block. One of the officers was able to close the D-Block access door, but then was immediately struck in the shoulder by gunfire. The escapees realized that their chances of escape were fading, and Shockley and Thompson retreated back to their cells to contemplate how to explain their involvement in the plan.