Complex sentence: Schindler had begun the separation process to leave the Navy, but his superiors insisted he remain on his ship until the process was finished, though he knew his safety was at risk, Schindler obeyed orders.
Split into simpler sentences: Schindler had begun the separation process to leave the Navy, but his superiors insisted he remain on his ship until the process was finished. Though he knew his safety was at risk, Schindler obeyed orders.