When we get a game idea it typically has one of these three elements already there, sometimes two, but very seldomly all three. So what you need to do after having the game idea with one of these, is to come up with the other parts.
You come up with the Mechanics. From here you could next think of the theme and the story to add these to your idea. Don't just take one, but come up with several alternatives.
Hey, why don't we do a "Weather" or "Pirate" game? This is when you start from the theme and you will need to think of the mechanics. You could try to come up with a story for the game even if you would never tell use it, but it would work for you on the background.
Try changing the theme and see here and here for more!
"The lost deceived boy encounters his nemesis and they fight over power". Your starting point can be the story, and to make it into a game, you'll need to have mechanics.
Also, you should understand how stories are told in games as you can't force them. See here for more!
Tetris is very mechanics oriented. One could create a theme by making the pieces have eyes to make them creatures. Our theme could then be a forest with creatures. The story could be that the creatures are in trouble and you need to help them before their forest gets crowded. The game would advance from situation to another in the forest.