Thaw the frozen chopped spinach and squeeze out all excess liquid until dry; set aside.
In a mixing bowl combine the drained spinach, 1 1/2 cups shredded mozzarella, grated Parmesan, cottage cheese, lightly beaten egg, minced garlic, Italian seasoning, salt, cracked pepper, and crushed red pepper; stir until well combined and set aside.
Bring a large pot of salted water to a boil and cook the jumbo pasta shells until just under al dente (about 1 minute less than package instructions). Drain, rinse with cool water to stop cooking, toss very lightly with a little olive oil to prevent sticking, and arrange in a single layer on a parchment-lined baking sheet.
Heat a large skillet over medium-high heat with a drizzle of olive oil. Add the diced onion and sauté until translucent, about 3–4 minutes.
Add the ground sirloin to the skillet, break it up, and cook until no longer pink, about 7–10 minutes; drain excess grease. Remove half of the cooked meat and stir it into the spinach-cheese mixture; reserve the other half for the marinara topping.
Preheat the oven to 350°F (175°C). Pour 1 1/2 cups marinara sauce into the bottom of a lightly sprayed 9×13-inch baking pan and spread evenly.
Mix the remaining cooked ground beef and onions into the remaining marinara to make the meat sauce for topping.
Stuff each cooked jumbo shell with about 2 1/2–3 tablespoons of the spinach, cheese, and meat filling and place the shells open-side up in the prepared baking pan in an even layer.
Pour the meat-marinara sauce over the stuffed shells to cover them, then sprinkle the remaining 1 1/2 cups shredded mozzarella evenly over the top and cover the pan with foil.
Bake covered for 25–30 minutes until bubbling, then remove the foil and bake an additional 10 minutes until the cheese is melted and slightly golden.
Sprinkle chopped fresh basil over the shells, let cool for 5–10 minutes, then serve.
