In a large soup pot, cook the bacon over medium heat until the bacon is crisp, 5-8 minutes. Using a slotted spoon, transfer the bacon to a paper towel lined plate. Add the onions and a pinch of brown sugar into the pot used to cook the bacon. Cook about 10 minutes, stirring frequently, until softened. At this point, slowly add in some of the beer, let it cook into the onions, add more and continue to cook. Do this until you have used 1/2 cup of beer or until the onions are caramelized to your liking and the beer has evaporated. Add the celery, jalapeño, garlic and thyme to the pot and cook over medium heat, stirring, until softened, 8 minutes. Add the other half of the remaining beer and cook until reduced by half, 5 minutes. Add 2 1/4 cups of chicken broth and bring to a simmer.
In a small skillet, melt the butter. Add the flour and cook over medium heat, stirring, until lightly browned, about 3 minutes. Slowly and carefully whisk this roux into the soup until incorporated and bring to a simmer. Cook the soup until thickened, about 8-10 minutes. Add the heavy cream, cheddar cheese + gruyere cheese and the remaining beer. Simmer, stirring occasionally, until thick and creamy, about 15 minutes. Stir in half of the bacon and season with salt and pepper. Ladle the soup into bowls and serve with the chili cheese popcorn, the remaining crumbled bacon and green onions.
To make the chili cheese popcorn whisk together the butter, chili powder, cumin and a good pinch of salt and pepper. Place the popcorn and crushed tortilla chips on a baking sheet and pour the butter mixture over the popcorn. Toss well. Sprinkle the popcorn with cheese and bake five minutes. Remove from the oven and serve warm with the soup.
*If you prefer to leave the bacon out just add 2 tablespoons butter or olive oil in it's place.