Cook the agnolotti according to package directions. Drain.
Meanwhile, bring the heavy cream and shallot to a boil in a large skillet over medium-high heat, stirring occasionally. Reduce the heat to medium-low and simmer to thicken slightly, about 2 minutes. Stir in the Parmesan and season with salt and pepper.
Layer half the agnolotti in a 9-by-11-inch baking dish. Top the pasta with the sliced tomatoes, basil and three-quarters of the mozzarella. Top with the remaining agnolotti and mozzarella. Pour the cream mixture over the top. Bake until golden and bubbly, 25 minutes. Cool slightly. Sprinkle Parmesan on top. Serve.
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