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1. Adjust oven rack to middle position and heat oven to 375 degrees. Microwave spinach in covered large bowl until completely thawed, about 15 minutes, stirring halfway through. Squeeze spinach dry, reserving 1/3 cup liquid. Pulse spinach in food processor until ground, 8 to 10 pulses, scraping down bowl every few pulses. Wipe out large bowl with paper towels. Transfer spinach to now-empty bowl; set aside.
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2. Heat oil in large saucepan over medium heat until shimmering. Add onion and cook until softened, about 5 minutes. Stir in garlic and pepper flakes and cook until fragrant, about 30 seconds. Add tomatoes, 1/2 cup processed spinach, 1 teaspoon salt, and 1/2 teaspoon pepper and cook until slightly thickened, about 10 minutes. Off heat, stir in 3 tablespoons basil; set aside.
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3. Process ricotta and reserved spinach liquid in food processor until smooth, about 30 seconds. Add Parmesan, remaining 3 tablespoons basil, eggs, 11/2 teaspoons salt, and 1/2 teaspoon pepper and process until combined. Stir ricotta mixture into remaining processed spinach.
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4. Cover bottom of 13 by 9-inch baking dish with 11/4 cups sauce. Top with 3 noodles and spread one-third of ricotta mixture evenly over noodles. Sprinkle with 2/3 cup mozzarella and cover with 11/4 cups sauce. Repeat twice, beginning with noodles and ending with sauce. Top with remaining 3 noodles, remaining sauce, and remaining 1 cup mozzarella.
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5. Cover pan tightly with aluminum foil sprayed with vegetable oil spray and bake until bubbling around edges, about 40 minutes. Discard foil and continue to bake until cheese is melted, about 10 minutes. Cool on wire rack for 30 minutes. Serve.
