Boil chicken breasts, drain, and shred then set aside. Place tomatoes into stockpot and cover with water. Bring to simmer then cook 8 minutes. Drain and peel.
Place peeled tomatoes, can of chipotle in adobo, garlic, and alt into blender and pulse until smooth.
Heat oil in large skillet and saute onions until tender. Add the pureed tomato mixture into pan along with oregano, marjoram, thyme, and simmer until thickened.
Add shredded chicken once sauce has thickened and stir to coat. Serve over rice or in tacos as desired.