The current meme originated in Metal Gear Solid 3. If the player kills a character that becomes important in the first two games, or waits too long at the Game Over screen, the game ends and Colonel Campbell of MGS1 and MGS2 fame yells Snake. What have you done?! You've created a time paradox!
It is sometimes used in reference to pictures containing two or more images of the same character.
TIME PARADOX can be seen written as PIME TARADOX. Often followed by Oh shi-.