Make the sponge by whisking together all of the ingredients (rye flour, cocoa, coffee, yeast, water, and molasses) in the bowl of a stand mixer or a medium to large sized mixing bowl.
1 cup (120 grams) dark rye or pumpernickel flour, 1 tablespoon cocoa, 1 tablespoon instant coffee, ½ teaspoon instant yeast, 1⅛ cup (255 milliliters) warm water, 2 tablespoons molasses
On top of the sponge, add the bread flour, additional cup of rye flour, and additional yeast.
2 cups (250 grams) bread flour, 1 cup (120 grams) dark rye or pumpernickel flour, ½ teaspoon instant yeast
Cover the bowl with plastic wrap and let it set at warm room temperature until the sponge is bubbling through, about 1 to 3 hours.
Mix the sponge and flours together, then add the vinegar, oil, and salt. Mix until the dough starts to come together, adding more bread flour or water as necessary to get a slightly sticky dough. Switch to the dough hook in your mixer once the dough comes together.
2 tablespoons cider vinegar, 2 tablespoons canola or other neutral vegetable oil, 1½ teaspoons salt
Knead for 5 to 6 minutes, add the caraway and fennel seeds, and knead for another 2 to 3 minutes until the dough is soft and stretchable.
1 teaspoon caraway seeds, 1 teaspoon fennel seeds
Form the dough into a boule, place it back in your mixing bowl, cover it with plastic wrap, and let it rise at warm room temperature until it has doubled in size, about 2-3 hours.
Grease a 9 inch by 5 inch loaf pan, shape your dough into a loaf, and place it seam down into the pan. Let it rise at warm room temperature until it has risen to about one inch about the sides of the loaf pan.
Meanwhile preheat your oven to 375°F.
Bake for about 40 to 45 minutes, until the internal temperature of the bread is 190 to 195°F.
Unmold immediately and let cool on a baking rack.