Arrange the eggplant and onions in a large shallow baking pan, brush the cut sides with 1 1/2 teaspoons of the oil and bake for 20 minutes.
Add the red pepper, tomatoes and garlic to the pan; brush the cut sides with the remaining 1 1/2 teaspoons of oil; sprinkle the thyme, basil, salt and black pepper over the vegetables and bake 20 minutes more or until tender.
Set aside the red pepper and 1 eggplant half.
Chop the remaining half eggplant, onions, tomatoes and garlic and transfer them to a large saucepan; add the stock, bring it to a boil, then lower the heat and simmer the mixture, stirring occasionally, for 20 minutes.
Meanwhile, peel the red pepper and dice the pulp. Dice the reserved eggplant.
In a food processor or blender, working in batches if necessary, whirl the cooked mixture until pureed.
Return the puree to the saucepan and stir in the diced eggplant and red pepper.
Simmer the soup for 5 minutes or until heated through.