Preheat oven to 425 degrees F (220 degrees C). Place the eggplant in a shallow, oven-safe dish, and bake for 1 hour until tender, turning every 15 minutes to ensure even cooking. Once done, remove, and allow the eggplant to cool until cool enough to handle.
Reduce the oven temperature to 350 degrees F (175 degrees C). Once the eggplant is cool enough to handle, cut it into 1/2 inch pieces, and combine with the tomatoes, onion, artichokes, garlic, parsley, chives, and basil. Pour into a baking dish
Bake uncovered in the preheated oven until the onions have softened, about 45 minutes.
Meanwhile, bring the quinoa and water to a boil in a saucepan. Reduce the heat to medium-low, cover, and simmer until the quinoa is tender, 20 to 25 minutes. To serve, spoon the eggplant mixture over the quinoa.