Thaw the frozen spinach and squeeze out all excess liquid until very dry; set aside.
In a mixing bowl combine the drained spinach, 1 1/2 cups shredded mozzarella, Parmesan, cottage cheese, beaten egg, minced garlic, Italian seasoning, salt and cracked 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 directions). Drain, rinse with cool water to stop cooking, toss very lightly with olive oil, and spread in a single layer on a parchment-lined baking sheet to cool.
Preheat the oven to 350°F (175°C).
Heat a large skillet over medium-high heat with a drizzle of olive oil. Sauté the diced onion 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 any excess grease and let the meat cool slightly.
Stir half of the cooked meat into the spinach-cheese mixture until combined; reserve the other half of the meat for the marinara sauce.
Pour 1 1/2 cups of marinara sauce into the bottom of a lightly sprayed 9×13-inch baking dish and spread evenly.
Mix the remaining cooked meat with the rest of the marinara to make a meat-topped sauce.
Stuff each cooled jumbo shell with about 2 1/2–3 tablespoons of the cheese-and-meat filling and place them open-side up in the prepared baking pan in a single layer.
Pour the remaining marinara-meat sauce evenly over the stuffed shells, then sprinkle the top with the remaining 1 1/2 cups shredded mozzarella. Cover the dish with foil.
Bake covered for 25–30 minutes until bubbly, then remove the foil and bake an additional 10 minutes until the cheese is melted and lightly golden.
Remove from the oven, sprinkle with chopped fresh basil, and let rest 5–10 minutes before serving.