First, slice the squash, zucchini and eggplant. Then, dice and fry in olive oil; the peppers, tomatoes, shallots and onions. Once the onions and peppers are softened, spoon the mixture in a baking dish. I chose to use small oven-safe dishes but really any baking dish will work.
Then, layer the sliced vegetables in an overlapping, alternating pattern. Be sure to cover the entire baking dish. Drizzle a bit of olive oil over the top.
Wrap, or cover, the baking dishes with parchment paper (not wax paper). This keeps the vegetables from drying out in the oven. Bake at 350F for about an hour. Remove from the over, let cool and refrigerate over night.
The next day, remove the parchment and cover the top with tomato sauce. Admittedly, I used tinned tomato paste with fresh sauteed vegetables to make the top sauce. I had only green tomatoes and those don't make an attractive sauce.
Return the sauce covered ratatouille to the oven for ~15 minutes to reheat. Serve while it's still hot. It's amazing on its own, but also goes well with rice and salad.