Scripts don't affect the game flow or the user interaction.
Scripts can only stop the game flow (at a very few specific predefined points), take the current game variables, modify the (small amount of) variables they are allowed to mess with and resume the game flow.
You can imagine the scripts as x-rays from space randomly changing some variables; or as parasites changing some specific (existing) function of an animal they have infected.
They can hack some values and change the damage of your weapon from 10 to 100... but they can't add a minesweeper easter egg when the user presses ctrl+alt+win+M during the opening cinematic
That's as good explanation as I can provide without writing a whole book about it.
Maybe it helps.