Preheat the oven to 375° F. Use a serrated knife to trim the tops off of the bagels. Run your knife around the center of each bagel, then use your fingers to press the insides back, creating a moat in the center of the bagel for your filling.
Chop the bacon and havarti cheese. Set aside.
In a medium bowl, whisk together eggs, heavy cream, salt, and pepper until smooth. Add the bacon, 3/4 of the cheese, and chives and stir to distribute.
Spoon the egg mixture into the bagels and then top each bagel with the remaining havarti cheese.
Bake for 15-17 minutes until the bagels are crisp and the cheese has melted. Serve immediately.