In one embodiment of the present invention, a method of treating a vascular occlusion located at a treatment site within a patient's vasculature comprises positioning an ultrasound catheter at the treatment site. The method further comprises delivering a microbubble therapeutic compound from the ultrasound catheter to the vascular occlusion during a first treatment phase. The method further comprises pausing the delivery of the microbubble compound and delivering ultrasonic energy from the ultrasound catheter in combination with other therapeutic compounds to the vascular occlusion during a second treatment phase while the delivery of microbubble therapeutic compound remains paused.