Set your Ninja multi-cooker or a heavy pot to high sear. Add a drizzle of olive oil and sear the quartered onion, tomatoes, and whole garlic cloves until lightly charred and fragrant. Remove and set aside.
Season the chicken thighs and breasts on both sides with fajita seasoning. In the same pot, sear the chicken on both sides until golden brown.
Return the seared vegetables to the pot with the chicken. Pour in both jars of salsa verde. Fill each empty jar with water, add 1 tablespoon of bouillon powder to each, shake well, and pour into the pot.
Cover and simmer on low for about 1 hour until the chicken is completely tender and falling apart.
Remove the chicken and set aside. Using an immersion blender, blend the tomatoes, onion, garlic, and remaining broth directly in the pot until smooth. This is your enchilada sauce. Shred the chicken and return it to the sauce or keep it separate for layering.
Preheat the oven to 350°F. In a large baking dish, spread a layer of enchilada sauce on the bottom. Layer corn tortillas over the sauce, then shredded chicken, more sauce, and a generous layer of the mixed Colby Jack and Pepper Jack cheese. Repeat the layers until the dish is full, finishing with a final layer of sauce and cheese on top.
Bake at 350°F for 45 minutes until hot, bubbly, and golden on top.
Serve warm with extra enchilada sauce and a dollop of sour cream.