In a large skillet, add enough olive oil to coat the bottom of the pan. Add chopped onions and sauté on medium heat until lightly golden brown, about 4-5 minutes.
Next add anchovy fillets (and any oil that comes with it from the jar) and use a wooden spatula to break down the anchovy in the olive oil. Then add chopped garlic and red pepper and continue sautéing for another 2 minutes so the garlic begins to deepen in color.
Next, add the red wine and allow to reduce slightly. Add the tomato sauce and water and stir everything together.
Add chopped olives and capers and let sauce cook on a simmer for 15-20 minutes. Taste for seasoning.
Once sauce is ready, add cooked pasta directly to sauce and toss together. Serve linguini puttanesca in large bowls and garnish with shaven Parmesan and fresh basil and crusty bread.