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Season chicken with salt and pepper.
Heat oil in a dutch oven, large saucepan or high-sided lidded skillet over medium-high heat.
Add chicken in a single layer and cook until browned, about 3 to 5 minutes per side.
Transfer chicken to a plate and set aside.
Reduce heat to medium.
Add onion, jalapeño and garlic to saucepan and sauté about 5 minutes or until softened.
Add tomato, chipotle and oregano and bring to a simmer for 8 to 10 minutes to let the flavors come together.
Transfer sauce to a blender and puree until smooth.
Return sauce to pan; season to taste with salt and pepper.
Add back chicken thighs, submerging in sauce as much as possible.
Partially cover and simmer for 20 minutes or until chicken is cooked through and tender, flipping once part-way through.
Remove chicken from sauce and shred with two forks, then stir back into thickened sauce.
To serve, spoon chicken and sauce onto a warmed corn tortilla.
Top with cotija cheese, red onion, cilantro and a squeeze of lime juice.