Unlike the original PC version, the Sega CD version displays an additional video sequence at the end of the game. After finally disabling the defender droid and destroying the Jeremiah O'Brian, the player is brought back to Starbase Amethyst expecting to be greeted as a hero for saving the world and stopping the war. Instead the player is brought to an interrogation room. The game ends with the player being locked in a chair while being tortured and interrogated by a Commanding Officer of Earth Force (the same that has been advising the player the entire time) about the player's knowledge of project Iron Helix.