Pour water and coffee into a microwave safe bowl. Stir in molasses and yeast, allow to stand for 10 minutes – it should get very bubbly.
In a large mixing bowl, combine flours, cocoa powder, caraway seeds and salt. Pour in yeast mixture and oil, stir well to combine.
Dump dough out onto a floured surface, knead until soft and elastic, 5-10 minutes. Place dough in a greased bowl, cover with plastic wrap, and allow to rise for one hour, or until doubled in size.
Once dough has doubled, punch it down, and divide it out. We divided the mixture into 8 equally sized balls, a medium-large bagel. You can divide into 6 for LARGE bagels, or 10- 12 for smaller bagels.
Preheat oven to 350 F. Line 2 baking sheets with parchment paper, scatter cornmeal across if desired. (Optional!)
There are two main ways of forming bagels – with roll each lump of dough into a thick “snake” and secure the ends together, or roll each lump into a smooth ball before poking a finger though. Once you have a hole made, stretch the ring of dough out a bit to enlarge the hole. Personally, I prefer the latter.
Once you have all of your bagels formed, set them on a baking sheet to rise for another 10 minutes.
In a large pot, combine water and honey, bring to a boil. I like to lay a sheet of parchment paper out across the other half of the stove, as my work surface.
Turn heat down a little, allowing water to simmer rather than continue to boil. 2 or 3 at a time, drop your bagels into the simmering water, allow to cook for 1 minute, then flip each and allow to cook for another minute. Drain well, place on the parchment lined work surface, allow to cool slightly.
Whisk egg together with 1 Tbsp of water, brush over the tops and sides of each bagel.
Combine remaining ingredients in a wide, shallow bowl. One at a time, pick up each bagel, gently invert into the bowl, and swirl around to coat the tops and sides. Place topping side up on baking sheets, as you finish each.
Bake for about 37 minutes (for 8), 35 minutes (if you’re making 10-12), or 40-45 mins (If you’re doing 6 large ones), until golden brown.