Complex sentence: Their goal was to frame Marks for the plane's hijacking and destruction, thus ruining the reputation of the Air Marshals Service, which they seek revenge against for allowing September 11 to happen in which Bowen's father died.
Split into simpler sentences: Their goal was to frame Marks for the plane's hijacking and destruction, thus ruining the reputation of the Air Marshals Service. Bowen wants revenge for the service allowing September 11 to happen, in which Bowen's father died.