Using a food processor, pulse the tomatoes for a few times making a coarse purée.
Bring a large pot of water to boil for the pasta.
In a large skillet combine the shallot and 1 clove of garlic with white wine. Bring to a boil and add the mussels.
Cover and cook for 2-4 minutes or until mussels open.
Transfer the open mussels to a bowl, cover pan, and repeat process until all mussels are open.
Let mussels cool down until it is easy to remove from the shells.
Remove half the shells and leave the other half intact. Transfer to a bowl and keep covered.
For the tomato sauce, place a strainer over another bowl and strain the liquid in the pan into a bowl. Reserve ½ cup. Rinse and dry pan.
Heat olive oil over medium heat in the pan and add 2 garlic cloves and pepper flakes. Cook, stirring for about 30 seconds. Add tomatoes, thyme, and sugar. Cook for 5-10 minutes until tomatoes have cooked down slightly. Add ½ cup broth from the mussels, stir and bring to a simmer. Taste and add salt as needed.
Add all mussels to sauce, cover and turn heat to very low. Keep warm while you cook the pasta.
When water is boiling, add salt and then pasta. Cook al dente following directions on the package.