If i understood you correctly, you need to use different scenes for each (one for intro, one for menu, and one ofr level one). Do not instance all three scenes into a main scene. Just the one you want to be loaded at start. Then, you can change scenes when animation ends, or a button is pressed, with something like this:
For example, in your main scene, you only instance the intro scene. When intro finish, change scene to menu. And when player press start (for example) in the menu, change to level 1. Do i explain myself?