Liberally salt and pepper both sides of chicken thighs. Bring 2 Tbsp. of olive oil to nearly smoking in a heavy bottom skillet. Brown the thighs on both sides and set aside.
Add the shallots and green pepper to the same pan and cook until the shallots just become translucent; about 5 minutes. Add the garlic and cook another minute.
Add 1/2 cup red wine to deglaze the pan, stirring up any bits of chicken left in the pan. Simmer for 15 more minutes to start reducing the wine.
Add the thyme, oregano, red pepper flake.
Stir in the canned tomatoes with their juices and 2 Tbsp. of tomato paste, and the black olives. Stir well to combine all.
If the sauce seems too thick, thin it with a little water, chicken stock or more red wine. Taste for seasoning and adjust. Cook the sauce for 30 minutes and then add the browned chicken.
Cover and cook at a low simmer for another 50 to 60 minutes until the chicken registers 165-170 on a meat thermometer.