Bloom water, yeast, and sugar in a bowl for 10 minutes.
Mix in whole wheat, butter, molasses, and honey with a wooden spoon or on low with a dough hook.
Add 1 cup of the AP flour, cocoa, and salt. Continue mixing.
Gradually mix in remainder of flour until dough pulls away from the sides.
Turn onto a floured surface and knead about 10 minutes until dough is soft and elastic.
Roll in an oiled bowl. Cover and rise 60-90 minutes.