If mushrooms are small,leave them whole; otherwise, half or quarter them; set aside.
Halve the squash lengthwise, then cut crosswise into 1/4-inch half rounds; set aside.
In a large skillet warm the olive oil over medium-high heat until hot but not smoking. Add the onion and garlic and cook until the mixture begins to brown, about 5 minutes.
Add the mushrooms,cherry tomatoes, tomato sauce, tomato paste, basil, thyme, salt and pepper and bring the mixture to a boil. Reduce the heat to low, cover and simmer for about 30 minutes.
Add the pasta to the boiling water and cook until al dente, 8 to 10 minutes.
Return the sauce to a boil over medium high-heat. Add the squash scallops and sour cream, and return to a slow boil. Cook, stirring, until the scallops are cooked through and the sauce has thickened slightly, about 4 minutes.
Drain the pasta and served topped with scallops and sauce.