Choices TellTale style, also I want to mix different game styles

How can I make a game with choices that affects the outcome of the story and have it in the background while i have another kind of gameplay, like I make a choice and after that in goes as a shooter and the choices are still there.

I would want to know how can i make choices (With that telltale timer) that affects the playstyle while being able to merge it with a different kind of game.

(My english is trash)