1. Preheat oven to 350. Halve the squash lengthwise and scrape out seeds. Place halves cut-side down on a sturdy rimmed baking pan and bake for 45-50 minutes or until flesh easily rakes into "spaghetti" with a fork. Set aside.
2. In a saute pan with a cover, warm the olive oil over medium-high heat until shimmering. Toss the mustard seeds in and cover the pan. Listen to the seeds pop and cook until popping stops, about a minute.
3. Set the lid aside and reduce heat to medium-low. Melt the butter in the pan and stir in the onion, garlic, jalapeno and cumin seeds. Season with salt (I like about a teaspoon of Kosher) and pepper to taste. Cook until onion is soft, 3-5 minutes. Pour in the tomatoes and stir until heated through, about 2 minutes.
4. Use a fork to scrape the flesh of the squash from its skin, raking apart the strands. Add the spaghetti squash to the saute pan and increase the heat to medium-high. Use tongs to evenly mix everything together and heat through, about 2 minutes.
5. Garnish with cilantro, if desired, and taste for more salt or pepper.