4 June, 1942

The Battle of Midway began. But the 6th Defense Battalion had been on the island for nearly 6 months. Upon hearing of the attack on Pearl Harbor, they immediately went to general quarters; however, no attacks transpired that day. That evening, two destroyers from the Imperial Japanese Navy, the Sazanami and Ushio began shelling the atoll for 23 minutes. One 5-inch battery from the 6th Defense Battalion engaged the destroyers during their second run until they departed the area. During this engagement, First Lieutenant George H. Cannon was mortally wounded; however, he refused evacuation while reorganizing his battery's command post. For his actions he was posthumously awarded the Medal of Honor. In total, ten marines from the battalion were killed in action and an additional ten more were wounded in action.

On 2 May 1942, Admiral Chester W. Nimitz spent the entire day at Midway inspecting the island. He spent a great deal of time with LtCol Shannon and inquired about what his defense battalion required in order to repel an amphibious assault. LtCol Shannon also assured Nimitz that if properly supported he could hold the island. Upon returning to his headquarters at Pearl Harbor, Admiral Nimitz wrote a joint letter to LtCol Shannon and Commander Cyril T. Simard, Commanding Officer of the Naval Air Station. He instructed both that they had been spot promoted to Colonel and Captain respectively, their garrison would receive his full support and he also let them know that he had intelligence that Midway was going to be attacked by the Japanese at the end of the month. Shortly thereafter, five additional antiaircraft batteries from the 3d Defense Battalion reinforced the island along with two companies from the Marine Corps' 2nd Raider Battalion. Battalion strength had swelled to nearly 1700 personnel by early June 1942. by At 0555 on the morning of 4 June 1942, 6th Defense Battalion's SCR-270 early warning radarpicked up a large force of Japanese aircraft approximately ninety miles out and approaching from 320 degrees. Thirty-six Japanese bombers eventually made it to Midway in two waves and were engaged by the guns of the reinforced battalion. Japanese after action reports detail losing three aircraft to antiaircraft fire that morning. The 6th Defense Battalion's battle standard can be seen in the early portions of John Ford's film  The Battle of Midway. The film also depicts members of the battalion engaging Japanese aircraft during the battle.

The 6th Defense Battalion remained at Midway for the remainder of World War II. Unlike all of the other defense battalions which were either decommissioned or had their coastal guns removed and were converted to anti-aircraft battalions, the 6th retained its moniker throughout the war. On 1 February 1946 the 6th Defense Battalion was re-designated as Marine Barracks, Naval Air Station Midway. The Marine Barracks was officially decommissioned on 31 October 1949