Cook brown rice pasta shells according to package instructions and set aside
In a medium bowl, combine tomato sauce, sour cream, and chopped chipotle peppers. Add green onions and stir again.
Add half of the noodles to your prepared baking dish. Top with half of the sauce, then sprinkle 1 cup of the grated cheese. Repeat with noodles, sauce, and then a final layer of cheese. Top with lots of fresh pepper and a sprinkling of chili flakes
Bake for 25 minutes, finishing with 3-4 minutes under the broiler to get a bit of crust on the cheese