Place chicken thighs, chicken stock, water, halved onion, garlic cloves, salt, and oregano in a large pot. Bring to a simmer over high heat; reduce to medium-low and cook, stirring occasionally, for 30 minutes. Remove from heat.

Transfer onion halves to a bowl with a slotted spoon; transfer chicken thighs to a separate bowl.

Pour broth through a strainer into a large bowl.

Heat olive oil in the same pot over medium heat. Add diced onions and cook until beginning to soften, about 4 minutes. Transfer strained liquid to onions. Bring mixture to a boil over high heat; turn heat to medium-low; reduce broth by about half, 15 to 20 minutes.

Transfer reserved boiled onions to a blender. Add chipotle peppers in adobo sauce. Swirl a bit of water in the can and add to the blender. Add tomatoes. Cover blender with the lid; pulse on and off until mixture is partially blended, then blend on medium speed until smooth, 1 or 2 minutes. Transfer to pot with broth and onions.

Increase heat to medium-high. Simmer 15 minutes or so, depending on how thick you want the sauce. Reduce heat to medium-low.