If you just want to desaturate one layer or layer group use the effect Grayscale and tween or lerp the intensity.
If you want to desaturate every layer below a certain layer, you can use the effect Saturation. Put it on a layer on top, this will turn the saturation of the layers below to the saturation of the pixels on this layer. Set that layer to not transparent, set the layer color to a grey and then tween or lerp the layer opacity.