1. Preheat oven to 325 degrees F (165 degrees C). Place squash halves cut side down on the baking sheet.
2. Bake squash 35 minutes in the preheated oven, or until a knife can be easily inserted. Remove from oven, and cool.
3. Meanwhile, saute the onion and garlic in olive oil until very soft. Stir in tomato juice, basil and black pepper. Bring to a boil and simmer until reduced to about 3 to 4 cups.
4. Remove squash strands with a fork or spoon (making sure not to pierce shell), reserving the shells.
5. Layer each half with a spoonful of the sauce, a layer of spaghetti squash strands, olives, and havarti cheese. Repeat layers until shells are full, or until all of the ingredients are used. Top with Parmesan cheese.
6. Bake for 20 minutes in the preheated oven, or until Parmesan cheese melts.