In the American version of the game, there is only one ending, where Apollo marries Maria, and the two live happily ever after. However, in the Japanese game, you are given a choice, and your choice determines the ending that you get to see.
In the Japanese version, you are given a box, and three options: open it, leave it closed, or throw it away. Leaving the box closed gives you the same ending as the American version, where you marry Maria. If you open it, you will return to your own home world, and you will notice a girl who looks just like Maria when walking on the beach, who you end up marrying and live happily every after. If you throw it away, you return to your home world, but you are struck by divine punishment, and never find Maria.