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Step 1
Heat oven to 425°. Line a rimmed baking sheet with a silicone baking mat or parchment paper. Place squash on baking sheet and drizzle with oil; rub to coat. Season with salt and black pepper. Turn cut side down and bake until a paring knife easily pierces skin and squash collapses easily under the pressure of tongs, 40–60 minutes, depending on your squash.
Step 2
Meanwhile, place tomatoes in a 3-qt. baking dish (any shape, such as an oval or a 13x9" rectangle works!) and squish with your hands to break tomatoes apart. Add garlic, sugar, ¼ cup oil, ¼ tsp. crushed red pepper flakes, ¼ tsp. kosher salt, and season with black pepper; stir to combine. Bake, stirring once or twice, until sauce thickens slightly and is bright red and bubbly, 35–40 minutes. Using a rubber spatula or spoon, coarsely mash garlic and any tomato pieces.
Step 3
Let squash cool slightly, then, using a fork, tease out flesh; discard skin. Add to baking dish with tomato sauce along with Parmesan. Stir to combine, breaking up squash further into strands. Season with salt and top with mozzarella.
Step 4
Return baking dish to oven and bake squash until cheese is melted, 5–7 minutes.
Step 5
Heat broiler. Broil, watching closely, until cheese is bubbly and browned, 1–2 minutes. Top with basil, more crushed red pepper flakes, and black pepper.