Kammala jumla mai zuwa: Yamaguchi ya koma Japan a takaice a ƙarshen Afrilu don kiyayewa a kan rundunarsa. A watan Yunin 1942, an tura shi zuwa
aikin Midway. A lokacin yakin, a ranar 6 ga Yuni, 1942, Yamaguchi bai yarda da kwamandan rundunar ba, Mataimakin Admiral Chūichi Nagumo. Wani jirgin sama mai leken asiri ya gano wani jirgin saman Amurka mai dauke da jirgin sama () kusa da Midway. A wannan lokacin, jiragen saman Japan sun kasance suna dauke da makamai don kai hari na biyu a Midway, tare da "Kate" masu saukar ungulu suna dauke da bama-bamai maimakon torpedoes. Yamaguchi ya yi kira da a kai hari nan da nan a kan jirgin Amurka, tare da jiragen da ke dauke da makamai kamar yadda suke, amma Nagumo ya yanke shawarar maimakon jira har sai an sake dawo da jiragen. Ba da daɗewa ba bayan haka, jirgin sama na Amurka ya hallaka dukkan masu jigilar Jafananci sai dai Yamaguchi's flagship "Hiryū". Yamaguchi da sauri ya ba da umarnin hare-hare biyu a kan "Yorktown" wanda ya gurgunta shi. "Hiryū" sannan jirgin sama ya hallaka daga, da kuma wasu jiragen sama na "Yorktown" marayu.