Born in Flensburg, Baagoe joined the Luftwaffe and was trained as a fighter pilot. He was assigned to "Zerstörergeschwader" 26 "Horst Wessel" (ZG 26—26th Destroyer Wing) and flew his first missions during the "Phoney War" period on the Channel Front. He claimed his first aerial victory during the Battle of France on 12 May 1940. He then participated in the Battle of Britain before transferring to the Mediterranean Front. On 20 April 1941, Baagoe became one of the pilots credited with shooting down the top Royal Air Force ace Marmaduke Pattle. On 14 May, Baagoe was shot down and killed in action at Heraklion, Crete. Posthumously, he was awarded the Knight's Cross of the Iron Cross.