How do I Freeze the game temporarily?

I was wondering how to freeze the game temporarily like in Super Metroid when you collect an upgrade, I tried using the timescale set to 0 and then set it back to 1 but a couple problems I had was inputs could still change the characters animation and also the timer wasn't working to set the timescale back up. This is the link to the c3p project. Also if anyone can figure out how to fix my crouch animation after collecting the boot upgrade my character can't stand back up normally how you're supposed to. dropbox.com/s/0n54upurzzy3nj3/Thing.c3p

Timescale is only really used for a pause screen where you press a key to action it. A timer won't work. Because what you're describing has no user input but is based on picking up an item better you block out all key presses for the player and then stop all animations if required.