Preheat the oven to 350ºF.
Sauté the onions over a medium heat until soft, about 5 minutes.
Add the tuna, cream, tomato paste, thyme, salt and pepper and stir until warm and blended.
Put the Zoodles into a 8"x8" baking dish and pour the sauce over the zoodles.
Top with cheese and bake for 20 minutes and then broil for about 2 minutes.