In a 5-quart pot, add olive oil and place over medium-high heat.
Once the oil is hot, add the onion and jalapeno. Cook for about 5 minutes or until the vegetables start to soften.
Add the ground beef, chipotle peppers, chili powder, unsweetened cocoa powder, kosher salt, black pepper, cumin, oregano, and smoked paprika. Stir to combine.
Cook the meat until it's browned. After it has cooked if there is a lot of grease in the pot feel free to drain the grease. If not, add the diced tomatoes and beef stock.
Simmer on low heat for about 90 minutes or until the chili is thick. You're looking for it to be about the thickness of sloppy joe meat. The chili will go inside tortillas, so consider that when figuring out when the texture of the chili is ready. Add more beef stock as needed if the soup cooks down too fast.
Cover the chili and remove from the heat.
Preheat oven to 350 degrees F.
Lay out your corn tortillas and add a little vegetable oil to a small skillet and place over medium heat. Add tortillas to the hot oil and cook for a few seconds on each side to help soften the tortilla. Add more oil to the pan between tortillas. Continue until all the tortillas have been softened.
Add 1/2 cup of the chili to the bottom of a 9x13 pan.
Lay out a corn tortilla, add 1 tablespoon cheese to the middle, and 2 tablespoons of the chili mixture.
Roll up and place seam-side down into the prepared dish. Continue until all the tortillas have been filled and put in the dish.
Top with remaining chili and cheese.
Bake for about 20 minutes or until the cheese is fully melted and browned.
Remove from the oven and sprinkle the top of the enchiladas with minced yellow onion and cilantro.