Step 1: Build a charcoal fire and let it burn down to embers. Lay the onion on the coals and char on all sides, turning with coals. Char the tomatoes and garlic the same way. This will take about 5 minutes for the onion and 2 minutes for the tomatoes and garlic. (The tomatoes should remain raw in the center.) Transfer to a platter and let cool, then scrape off most of the burnt skin (leave a little for color). Cut the charred vegetables into 1 inch pieces.
Step 2: Place the charred vegetables, chipotle, and cilantro in a food processor and coarsely puree. Work in the lime juice and salt and pepper to taste. Transfer the salsa to a bowl for serving.