Preheat your oven to 350°F and grease a 9x13 inch baking dish with butter or cooking spray. While the oven heats, mince one jalapeño finely and slice the other into thin 1/8-inch rounds, keeping them separate. Thinly slice the scallions and set aside. If your cream cheese isn't already chilled and cubed, cut it into small cubes now—cold cream cheese will distribute better throughout the casserole and create nice pockets of richness.
In a large bowl, whisk together the eggs, heavy cream, garlic powder, kosher salt, and black pepper until well combined and slightly frothy. The cream and eggs should be fully incorporated with no streaks of white visible. This creates a smooth, custard-like base that will cook evenly throughout the casserole.
Spread half of the cooked crumbled bacon (about 1/2 cup) across the bottom of your prepared baking dish. Sprinkle 1 cup of the grated cheddar cheese evenly over the bacon, then distribute the minced jalapeño throughout this layer. Pour the egg custard mixture from Step 2 over everything, stirring gently with a fork to distribute the ingredients evenly without creating air pockets. Place in the preheated 350°F oven and bake for exactly 15 minutes—the eggs will still be slightly underset, which is intentional.
Remove the casserole from the oven after the 15-minute initial bake. I like to scatter the cubed cream cheese directly onto the surface rather than mixing it in—this way it melts into little pockets of richness instead of blending into the eggs. Distribute the remaining 1 cup of grated cheddar cheese evenly across the top, then scatter the remaining 1/4 cup crumbled bacon and all the sliced jalapeño rounds. Return to the oven and bake for 30-35 minutes until the eggs are completely set and the top is golden brown and bubbling slightly at the edges.
Remove the casserole from the oven and let it rest for 3-5 minutes—this allows the residual heat to set any barely cooked spots and makes it easier to cut clean portions. Scatter the sliced scallions evenly over the top just before serving. For a spicy kick, sprinkle the red pepper flakes over individual servings rather than the whole casserole so guests can control the heat level.