A pulmonary embolism (PE) is an obstruction in a pulmonary artery, and a saddle PE occurs when the obstruction is lodged in the main pulmonary trunk and spans the left and right pulmonary arteries. The current case study describes complications of a thrombus in transit across a patent foramen ovale (PFO). A 35-year-old female presented to the emergency department after a nontraumatic syncopal fall. She had recently returned from a cross-country flight 10 days before and had noticed left calf tenderness when exiting the plane. Vitals were notable for sinus tachycardia at 120 bpm. An electrocardiogram indicated an S1Q3T3 pattern, and chest computed tomographic angiography was positive for a saddle PE. A 2D (twodimensional) transthoracic echocardiogram showed right ventricular free wall hypokinesis and McConnell's sign. Echocardiogram findings were concomitant with a thrombus in transit across the interatrial septum, indicating a possible PFO. An emergency pulmonary embolectomy with cardiopulmonary bypass and closure of her PFO was performed the following morning and complicated by cardiogenic shock and subsequent cardiac arrest. The patient was resuscitated in the operating room but failed to be removed from cardiopulmonary bypass, requiring low-dose inotropic support and venoarterial extracorporeal membrane oxygenation flow at 4 L/min. After a repeat right pulmonary artery thrombectomy and two subsequent transesophageal echocardiograms indicated stable right ventricular systolic function, decannulation was performed. The patient was discharged on day 17 with long-term anticoagulation and home healthcare. In the current case report, the patient's unstable and deteriorating condition was complicated by unusual findings of a thrombus in transit across a PFO. These additional echocardiogram findings represented an unusual case that warranted surgical treatment instead of systemic thrombolysis therapy because of the increased risk of systemic clot embolization.