Heparin-induced thrombocytopenia (HIT) is characterized clinically by thrombocytopenia, hypercoagulability, and increased risk of thrombosis, and serologically by the presence of antibodies against platelet factor 4 (PF4). We present a 27-year-old male with persistent holocranial headache and depersonalization, initially attributed to thrombocytopenia following a positive Dengue virus serology. Despite no initial evidence of ischemia on imaging, subsequent findings included extensive venous thrombosis in the right lower limb, contraindicating immediate anticoagulation. The patient later developed a left lacunar ischemic stroke with hemorrhagic transformation and bilateral pulmonary thromboembolism. Examination findings revealed right hemibody weakness and dysplastic megakaryocytes on bone marrow aspirate. This case highlights the diagnostic challenges and clinical complexities in managing thrombotic events associated with thrombocytopenia and viral infections.