For the sauce, to a saucepot over medium heat, add olive oil, onions and garlic. Sweat for 10 minutes, until soft and tender. Add chili flakes and cook for an additional 3 minutes. Add the tomatoes, adobo sauce, oregano and basil sprigs, and bring to a simmer. Simmer for 2 1/2 hours stirring frequently. Remove from heat, season with salt to taste.
Lightly poach eggs in simmering water.