Prepare cake mix according to package directions. Fill greased muffin cups 2/3 full and bake at 350 degrees for 15 to 20 minutes. Cool completely.
Whisk pudding mix and milk for 2 minutes; let stand 5 minutes. Use a serrated knife to cut off the top of each cupcake; set tops aside. Stir 1/2 cup whipped topping into pudding.
Spoon one tablespoon onto each cupcake; replace cupcake tops. In a microwave-safe bowl, combine remaining whipped topping and chocolate.
Microwave for one minute; stir and microwave an additional 30 seconds. Stir until chocolate is melted; let stand 15 minutes. Frost cupcakes with chocolate mixture.