Bring a large pot of salted water to a boil and cook the whole wheat penne until al dente according to package directions; drain and set aside.
While the pasta cooks, heat 2 tablespoons olive oil in a large sauté pan over medium-high heat.
Add the sliced red onion and minced garlic to the pan and cook until the onion softens, about 2 minutes.
Add the sliced red, orange, and yellow bell peppers and the turkey sausage rounds; cook, stirring occasionally, until the peppers are tender and the sausage is heated through, about 3–5 minutes.
Season the mixture with crushed red pepper, salt, and black pepper to taste.
Transfer the drained pasta to a large serving bowl. Stir in the sausage and pepper mixture, then add the halved grape tomatoes, shredded Parmesan, and chopped basil; toss to combine.
Adjust seasoning if needed and serve immediately.