Preheat oven to 375º. In a large pot of boiling salted water, cook pasta, stirring occasionally, until very al dente, 2 to 3 minutes less than package instructions. Drain pasta and return to pot. Toss with marinara and set aside.
In a large, high-sided, ovenproof skillet over medium-high heat, heat 1 tablespoon oil. Add sausage and cook, tossing occasionally, until golden on both sides, about 3 minutes. Transfer sausage to pot with pasta.
In same skillet over medium-high heat, heat remaining 2 tablespoons oil. Cook zucchini, bell pepper, black pepper, and ½ teaspoon salt. Cook, stirring occasionally, until golden and vegetables are crisp-tender, about 3 minutes.
Add garlic to skillet, and cook, stirring, until fragrant and golden, about 1 minute. Add spinach and cook, tossing, until wilted, about 2 minutes more. Scrape vegetable mixture into pot with pasta, add basil, and toss to combine; reserve skillet.
Spoon half of pasta mixture into reserved skillet. Top with 1 ½ cups mozzarella. Scrape remaining pasta mixture over and top with remaining 1 ½ cups mozzarella.
Bake until cheese is melted and top is golden brown, 14 to 16 minutes. Let cool 5 minutes. Top with more basil before serving.
