Line a baking sheet with aluminum foil. Cut the bagels horizontally, separating the top and bottom sides. Place them face up on the lined baking sheet.
Spread 1 tablespoon of pizza sauce on each bagel slice.
Divide ½ cup of the mozzarella between 6 of the bagel slices.
Scatter pepperoni over the mozzarella cheese.
To make the topping for the other bagel slices, add the fontina and Parmesan to the remaining ¼ cup of mozzarella and combine.
Sprinkle the cheese mixture over the last 6 bagel slices.
Place the bagels in the oven and cook for 12 minutes or until the cheese is bubbly and lightly golden.
Remove from the oven and garnish the 3-cheese bagel bites with basil. Serve immediately.