In early 1934, Cowley was sent by
J. Edgar Hoover (as head of the "Flying Squad") to Chicago specifically to aid the FBI pursuit of
John Dillinger. The Chicago Agents initially resented Cowley as a desk jockey who was infringing on their territory and driving them too hard. However, Cowley soon established a reputation as one who drove himself as hard as he drove his agents. The relationship between Cowley and
Melvin Purvis was complex and is debated by historians. Fans of Purvis tend to downplay Cowley, and the official FBI records tend to play down Purvis, as Hoover preferred Cowley. Cowley and Purvis worked together as a team. Individually neither one of them could have caught Dillinger, but together they concentrated on the areas that they knew best: Cowley on gathering intelligence and Purvis working the field. A squad of agents under Cowley worked with East Chicago policemen in tracking down all tips and rumors. It was Cowley who cut the deal with
Ana Cumpănaș, the so-called "Woman in Red". Cowley seems to have understood this relationship. After Purvis's botched raid on
Little Bohemia Lodge, Purvis went on a drinking spree, and Cowley hushed it all up. During the Dillinger stakeout, Cowley was in charge of the team at the Marbro Theater, while Purvis' team was at the
Biograph Theater. At 8:30 p.m., Sage, Dillinger and Polly Hamilton strolled into the Biograph Theater to see
Clark Gable in
Manhattan Melodrama. Purvis phoned Cowley, who shifted the other men from the Marbro to the Biograph. Later, after Dillinger was killed, Purvis was in one room, holding a press conference and Cowley was in the next room reporting to Hoover over the phone. Hoover kept telling Cowley to break up the press conference, but Cowley refused. ==Death==