Create a var variable (fade_progress) in your script which handles the fade in/ out stuff, then write
float fade_progress_var;
at the beginning of your fx file.
Now put
NOISE_EFFECT = lerp(NOISE_EFFECT,1,fade_progress);
before the Color *= NOISE_EFFECT line.

I assume that fade_progress is in 0..1, otherwise (if you want to keep it in the interval 0..100) write (fade_progress/100) as the 3rd argument in lerp.