Preheat oven to 400°F Cut spaghetti squash in half lengthwise. Remove and discard seeds. Place squash, cut sides down, in a 13- x 9-inch pan, and add water to a depth of 1/2 inch. Roast in a preheated 400°F oven for 30 to 40 minutes or until lightly browned on the outside.
Drain and cool slightly. Remove spaghetti-like strands from the squash using a fork, place in a bowl and set aside. Discard the squash shells.
Sauté onion and garlic in a large nonstick skillet coated with vegetable cooking spray until tender. Stir in tomato, green chilies, chili powder, ground cumin and red pepper flakes. Cook until thoroughly heated.
Add squash to the skillet and cook, stirring gently, until thoroughly heated.