A case of the syndrome of the trephined progressing to paradoxical herniation is presented in a patient with a penetrating brain injury, postdecompressive craniectomy, and a delayed cerebral spinal fluid leak from a skull base defect. The patient had a penetrating head trauma from a high-velocity ballistic projectile during military wartime operations. The patient's clinical course, which demonstrates a rare presentation of central sleep apnea syndrome or Ondine's curse, is reviewed. Radiographic imaging includes sequential computed tomography (CT) scans with and without intrathecal contrast. Medical management was directed at increasing the intracranial pressures (ICPs) by placing the patient into Trendelenburg position and increasing hydration. Surgical intervention involved correction of the skull base defect by intranasal endoscopic repair. A literature review of paradoxical herniation and delayed neurologic decline in postcraniectomy patients is conducted, and the surgical and neurocritical care management is discussed.