Purée tomatoes, coffee, onion, garlic, chipotle, and 1 tablespoon oil in a blender until smooth. Simmer purée in a 10-inch heavy skillet, stirring occasionally, until thickened, about 10 minutes. Stir in chocolate and season with salt. Remove from heat.
While sauce simmers, fry eggs in 2 batches in remaining tablespoon oil in a 12-inch nonstick skillet over moderate heat until cooked as desired. Serve eggs topped with sauce.
