1Preheat the oven to 350°F. Lightly dampen a paper towel with a small amount of olive oil and wipe a rimmed baking sheet with it.
2Place the squash, cut-sides down, on the prepared baking sheet. Prick all over with the tip of a knife. Bake until very tender, 28 to 30 minutes.
3Remove from the oven and let cool for 5 minutes. Turn the squash over and using the tines of a fork, scrape out the flesh - it will come out in long, thin, spaghetti-like strands.
4Heat the 2 tablespoons of oil in a large skillet over medium-high heat.
5Add the onion and thyme; cook, stirring occasionally, until softened and starting to brown, 6 to 7 minutes. Add the bell pepper until tender, 4 minutes.
6Add the capers and cook for 1 minute. Stir in the squash and cook, tossing, until hot and well mixed, 1 to 2 minutes.
7Remove from heat and season with salt and pepper.