Heat the oven to 350°F. Heat 3 tablespoons olive oil in a large frying pan over medium-high heat until shimmering. Add 1 diced onion and 2 minced garlic cloves, then season with kosher salt and freshly ground black pepper to taste. Cook, stirring occasionally, until softened.
Remove 3 spicy Italian sausage links (about 1/2 pound) from their casings and add them to the onions. Cook until browned, breaking the sausage into small pieces with the back of a spoon. Season again with kosher salt and freshly ground black pepper to taste.
Add 1 (28-ounce) can fire-roasted crushed tomatoes, 2 tablespoons finely chopped oregano, 2 teaspoons chopped thyme, and 1 cup dry long-grain white rice (like Jasmine or Basmati). Reduce the heat to medium-low and simmer, stirring frequently to keep the rice from sticking, until a spoon leaves a mark on the bottom of the pan and the mixture doesn't immediately fall back in on itself. Remove from the heat.
Stir 1 cup of the shredded mozzarella and 1 cup shredded Parmesan into the sausage and rice mixture, then stir in 1/2 cup pesto sauce. Taste—the rice will still be a little crunchy—and add more salt or pepper if needed. Set the filling aside while you prepare the peppers.
Slice 4 medium red, orange, or yellow bell peppers in half vertically, keeping the stems intact. Remove the seeds and white ribs with a paring knife, tap out any remaining seeds, and arrange the pepper halves snugly in a 9 x 13-inch baking dish.
Divide the sausage filling among the pepper halves, pressing it down gently to fill all the nooks and crannies. You may have a little filling left depending on the size of the peppers, but you should use almost all of it.
Pour about 2 cups water, or enough to reach about 1/4 inch up the sides of the peppers, into the bottom of the baking dish.
Bake uncovered for 30 minutes. Remove from the oven, sprinkle the peppers with the remaining 1/2 cup shredded mozzarella, and return to the oven for another 30–45 minutes, or until the rice and peppers are tender and the cheese is golden brown.
Transfer the peppers to a serving dish, drizzle with additional olive oil if desired, and garnish with fresh basil leaves and additional Parmesan. Serve and enjoy!