If the player chooses to save the cube Vaughn and his crew are seen leaving the planet and the game ends.
If the player finds the secret codes in the factory they can choose to blow up the planet. Picking this will lead to a timed escape sequence and a scene of them flying away from the exploding planet followed by a bonus scene.
The bonus scene involves the crew on the cube planet being celebrated for their bravery. The game end.
If the player chooses to kill the cube Vaughn will kill the cube and will take Rook off the planet. He'll drop Rook off at home and the game will end with him walking back into his cabin.