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In 1942 Stover flew with VF-8 aboard Hornet at Midway and then transferred to VF-5, with which he participated in the Guadalcanal campaign.

When the new Yorktown was commissioned in 1943, Stover was assigned to the Radar Plot as a Fighter Director Officer. However, he pushed hard to be allowed back to his old squadron, VF-5, and eventually succeeded that December. On 17 February 1944, flying with VF-5 in an attack on Truk, his aircraft was shot down by AA, and though he managed to bail out and take to his raft, he was captured by the Japanese and executed.