Preheat oven to 400 and roast eggplant until soft but not mushy, about half an hour.
Cut eggplants in half and scoop out the pulp. Chop the pulp roughly and place in a bowl.
Heat skillet on high, add the olive oil, onions and garlic and cook until onions are soft, 5 to 7 minutes. Add mushroom and cook until golden brown and all liquid has evaporated. Add carrots and red peppers and allow to cook 2 more minutes. Add to the bowl of eggplant and combine with the bread crumbs, salt, pepper and fresh chopped basil. Mix well.
Spread half the marinara sauce onto the bottom of ovenproof baking dish. Spoon stuffing into the eggplant and place in baking dish, cover with the rest of the marinara sauce.
Cover and bake at 350 for 30 minutes.