In the integrated aircraft routing, crew scheduling and flight retiming problem, a minimum-cost set of aircraft routes and crew pairings must be constructed while choosing a departure time for each flight leg within a given time window. Linking constraints ensure that the same schedule is chosen for both the aircraft routes and the crew pairings, and impose minimum connection times for crews that depend on aircraft connections and departure times. We propose a compact formulation of the problem and a Benders decomposition method with a dynamic constraint generation procedure to solve it. Computational experiments performed on test instances provided by two major airlines show that allowing some flexibility on the departure times within an integrated model yields significant cost savings while ensuring the feasibility of the resulting aircraft routes and crew pairings.