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1
Preheat oven to 375 degrees F. Pour tomato puree into bottom of a 10-inch oval baking dish
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2
Place the sliced garlic cloves and chopped onion into the sauce.
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3
Stir in the oregano, crushed red pepper flakes, one tablespoon of the olive oil, and season generously with salt and pepper.
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4
Trim the ends off the eggplant, zucchini, and yellow squash. Trim the top of the red pepper and remove the core. On a mandoline, adjustable-blade slicer, or with a very sharp knife, cut the eggplant, zucchini, yellow squash, and red pepper into very thin slices, approximately 1/16-inch thick.
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5
Atop the tomato sauce, arrange vegetable slices concentrically from the outer edge to the inside of the baking dish. Overlap them, alternating vegetables and leaving just a sliver of the flat surface of the bottom vegetable visible.
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6
Drizzle the remaining tablespoon of olive oil over the vegetables and season them generously with salt and pepper. Remove the leaves from the thyme sprigs with your fingertips and sprinkle over the dish. Cover with a piece of parchment paper cut to fit inside the baking dish.
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7
Bake for approximately 45 to 55 minutes, until the vegetables release their liquid and are just cooked though-you want them to retain some structure rather than being completely limp. They should not be brown at the edges, and you should see that the tomato sauce bubbling up around them.
