Cook the bacon in a small skillet over medium heat until cooked through and crispy. Place the bacon on paper towels to drain the grease then chop it into bits.
Remove all but 1/2 teaspoon of bacon grease from the same skillet (or add 1/2 teaspoon of butter) and add the shallot, crushed red pepper flakes, sea salt, and freshly cracked pepper, to taste. Cook, stirring constantly, for 1-2 minutes or until the shallot is tender. Remove from the heat.
Fill a small skillet with enough water to come up to about 3/4 of the way up the side of the ramekin and heat over high until boiling.
Butter the ramekins well, then divide the bacon crumbles and sauteed shallots evenly in the ramekins.
Add 2 teaspoons of finely grated parmesan and 1/2 teaspoon of heavy cream in each ramekin.
Crack one egg in each ramekin carefully so you don’t break the yolk. Run the edge of a small rubber spatula through the egg whites a few times, being very careful not to break the yolk. (This allows the egg whites to cook faster and more evenly).
Once the water is boiling, turn off the heat and carefully add the egg-filled ramekins to the skillet, cover with a lid, turn the heat back up, and cook for about 6-8 minutes (depending on egg size), or until the whites are set and the yolks are soft. Watch them carefully so they don't overcook.
Turn off the heat and carefully remove the ramekins with tongs. Season with sea salt and freshly cracked pepper, to taste, and top with fresh chives.
Serve immediately with buttered toast if desired. Enjoy.