In 1940, when the novitiate was invaded and everyone was gathered for transport to the concentration camps, Frąckowiak escaped. He went to Jarocin and partook in underground religious ministry and created an editorial, "For you, Poland". The Nazis knew about the secret group, however, and they were hunted down and captured with some members that managed to escape. He asked to be the one found solely responsible and taking all the blame in hopes of liberating some of the members. He was tortured and imprisoned in Fort VII, and was then transferred to Dresden in 1943, where he was beheaded by guillotine on May 5, 1943, after secretly writing a letter to his family. He was thrown in an unmarked grave.