Preheat oven to 375 degrees.
In a nonstick skillet, cook chopped bacon until crispy. Remove with a slotted spoon and place on a paper towel-lined plate.
Discard all but 1 tablespoon bacon grease. Add onion and cook over medium high heat until onion is soft. Let cool.
In a medium bowl whisk together eggs, cream cheese, and half-and-half. (Cream cheese does not have to be smooth, but break it down as much as possible.)
Stir in chopped canned jalapenos.
Set aside 1/2 cup cheddar cheese and stir in the rest of cheddar and the Monterey Jack cheese into the egg mixture.
Season egg mixture to taste with black pepper.
Stir in onions.
Scatter bacon pieces on bottom of pie crust.
Pour egg mixture on top.
Arrange jalapeno slices on top and sprinkle with the 1/2 cup cheddar cheese that was set aside.
Place on baking sheet and bake for 40 minutes. Serve warm, at room temperature, or chilled.