Place bacon in a heavy pot and cook over medium-high heat, turning occasionally, until fat begins to render, about 5 minutes. Drain off 1/2 of the bacon grease.

Reduce heat to medium and add onion. Cook, stirring often, for about 5 minutes. Add garlic, red pepper flakes, salt, and pepper; cook and stir for 2 minutes.

Increase heat to high and immediately pour in 3 cups water. Bring to a boil, stirring to scrape up browned bits from the bottom of the pot. Add chopped collard greens and 1 more cup of water. Bring back to a boil. Reduce heat and simmer until greens are tender, about 1 hour.