Braid is an indie platformer, and one of the first titles to really take advantage of the desire for retro gaming. A deliberate throwback to old school SNES and arcade games that willfully ignore player questions and desire to learn more about lore, it presents itself as a simple "rescue the princess"-style journey, with most of the backstory provided by the player.
Still, like those old-school games, Braid also hides a ridiculously difficult-to-achieve secret: by collecting the seven stars hidden in each level (there is no indication in the game itself that there are hidden stars to collect), players can unlock the secret ending. Oh, one more thing: one of the stars is only collectable by waiting on one screen for over TWO HOURS without pressing pause.
Once the secret ending is collected, the princess explodes after a famous Oppenheimer quote appears on the screen: "I am become death, destroyer of worlds." It sure seems Braid is implying that the player's quest for the princess was actually about a player's quest for nuclear armament, a decidedly dark turn for a seemingly simple platformer.
Jonathan Blow eventually confirmed this theory, sort of, by reaffirming that everything in the game is there for a reason when asked about the famous quote. "I'm not really talking that much about the story, but [that quote is] most certainly in there," he teased. "It's something to take into account when reading the text. But how much does it come into the actual story? It's a very tightly focused game, I spent three years working on details."