Start by combining the yeast and flour in a large mixing bowl. Add the water, stirring just until combined. The sponge will be very sticky, thick and look almost like pancake batter. Cover with plastic wrap and let this sit for 2 hours or until bubbles appear on top of the sponge. It should almost double in size and collapse when the bowl is tapped on the counter.
1 1/2 teaspoons instant yeast, 4 cups (510g) bread flour, 2 1/2 cups (567g) room temperature water
Once the sponge is bubbly and foamy looking, sprinkle the additional 1/2 teaspoon of yeast on top and stir. Add 3 cups of the flour along with the brown sugar and salt. Mix on low speed with the dough hook or with a sturdy wooden spoon until the dough starts to form into a bowl. Gradually add the remaining 3/4 cup of flour to the dough until it is fairly firm and only slightly tacky.
1/2 teaspoon instant yeast, 3 3/4 cups (482g) bread flour, 3 teaspoons table salt, 1 Tablespoon dark brown sugar
Knead for at least 6-8 minutes with the dough hook attachment or 10-15 minutes by hand to develop the gluten. The dough should be firm, but still pliable and smooth. It should pass the windowpane test where you pinch off a smallish piece of dough and stretch it between your fingers. You should be able to see light through the dough without it tearing. If the dough tears while stretching, add a little water (maybe 1-2 tablespoons at a time) and keep kneading the dough for another 1-2 minute before testing again. If the dough is too sticky, add more flour (maybe 1/4 cup at a time) until the dough is fairly stiff and firmer than most other bread dough. It should be pliable but not so tacky that it sticks to the countertop or your fingers.
Use a bench scraper or sharp knife to divide the dough into twelve even pieces that are each about 4 1/2-ounces (128g). Roll the dough pieces into tight balls, then cover with plastic wrap or a damp towel and let them to rest for 20 minutes to allow the gluten to relax.
Cut 12 squares of parchment paper and set aside. Poke a hole in the center of each ball of dough and use your fingers to evenly stretch the hole until it is about 2 1/2-inches in diameter. Remember that the whole should look larger than you think it will because it will shrink when baking.
Place each shaped bagel on a square of parchment paper and arrange on a full-size baking sheet. Loosely cover with plastic wrap and let the bagels rest for 20 minutes on the counter at room temperature.
Transfer the bagels to the refrigerator to slowly rise overnight (at least 8 hours or up to 2 days). This allows the flavor of the bagel to develop and is worth the wait, although you could let them rise for 60-90 minutes at room temperature, then boil and bake at this point if you desire. I like to make my bagels the night before and bake them fresh in the morning anyway, so this overnight retard approach is my preferred method anyway.
When you are about ready to bake the bagels, preheat the oven for at least 20 minutes to 425℉ (218℃). Line a full-size baking sheet with parchment paper and sprinkle with cornmeal or semolina flour. Fill a wide pot with water and let it come to a full rolling boil on the stovetop. Add the honey, brown sugar, or barley syrup.
2 quarts water, 2 Tablespoons honey, Cornmeal or semolina
Remove the bagels from the fridge and carefully drop 2 to 3 of them into the boiling water. Boil for 1 minute, then flip them over and boil on the other side for another minute. If you want extra chewy bagels, you can boil for 2 minutes per side. Remove the boiled bagels from the water using a slotted spoon and arrange on the prepared baking sheet. Sprinkle the bagels with your toppings, if using, as soon as they come out of the water so the toppings will stick. Repeat with the remaining bagels.
Toppings like sesame seeds, poppy seeds, kosher salt, dried minced garlic or onion, or everything bagel seasoning, grated Asiago, parmesan, cheddar cheese, or melted butter with cinnamon sugar (added after baking)
Bake for 14-20 minutes, rotating the pan partway through. The bagels should be a light golden brown, although you can bake them slightly longer if you prefer them darker in color.
Let the bagels cool for at least 20 minutes before slicing and serving.