Bring a large pot of well-salted water to a rolling boil. Add the pasta and cook until 70–80% done, leaving a firm bite.
Before draining, reserve about 1 cup of pasta water. Drain the pasta and set aside.
Heat olive oil in a pan over medium heat.
Add the chili flakes and sliced red jalapeños and sauté briefly, stirring continuously so they release flavor into the oil without burning.
Add the cinnamon and nutmeg powder. If the spices begin sticking to the pan, add a small splash of water or pasta water.
Pour in a small amount of reserved pasta water to deglaze the pan and allow the flavors to blend.
Add the partially cooked pasta to the pan and toss to coat it in the chili-infused liquid.
Sprinkle in the oregano and thyme mixture and mix evenly.
Add more pasta water as needed and continue cooking the pasta over medium heat, stirring occasionally.
Allow the liquid to reduce gradually so it forms a light, glossy coating on the pasta instead of a heavy sauce.
Cook until the pasta is fully done and most of the liquid has evaporated.
Remove from heat and serve immediately.
Top with freshly grated Parmesan cheese if desired.