1. Heat 2 tablespoons of the olive oil in a large, heavy skillet over medium-low heat. Add the onions and stir until they begin to soften (3-4 minutes).
2. Add garlic, bay leaf, thyme, and pepper. Stir everything together, turn the heat to low, cover and cook until the onions become a golden brown puree (45 minutes). Stir often, adding water as needed to prevent sticking.
3. Remove bay leaf and stir in the capers. If there is liquid in the pan, cook over medium heat, uncovered, until it evaporates.
4. Preheat the oven to 450 degrees F.
5. Roll out the pizza dough and place on a 12" or 14" pizza pan or large baking sheet. Brush the remaining tablespoon of oil over the bottom but not the edge of the crust. Spread the onions over the crust in an even layer. Top with anchovies and olives. Bake until crust is starting to brown (15-20 minutes).