Season the chicken thighs on both sides with salt and pepper.
Heat 1 tablespoon vegetable oil in a Dutch oven or large high-sided skillet over medium-high heat.
Add the chicken in a single layer and brown for about 3–5 minutes per side; cook in batches if needed so pieces brown evenly. Transfer browned chicken to a plate and reduce heat to medium.
Add the chopped onion, seeded and chopped jalapeño, and minced garlic to the pan and sauté about 5 minutes, until softened.
Stir in the fire-roasted diced tomatoes, 2 tablespoons chopped chipotle peppers in adobo, and 1 teaspoon dried oregano; bring to a simmer and cook 8–10 minutes to concentrate the flavors.
Carefully transfer the hot sauce to a blender and puree until smooth, or use an immersion blender in the pot; return the sauce to the pan and taste, seasoning with salt and pepper as needed.
Add the browned chicken back to the sauce, submerging the pieces as much as possible, partially cover, and simmer over medium-low heat 20 minutes, flipping the chicken once halfway, until cooked through and tender.
Remove the chicken to a plate, shred with two forks, then stir the shredded chicken back into the thickened sauce.
To serve, spoon the saucy shredded chicken onto warmed corn tortillas and top with crumbled cotija, thinly sliced (or pickled) red onion, fresh cilantro, and a squeeze of lime.