Cut one onion in half without peeling. Peel and finely chop the second onion.
heat a large heavy-based skillet, add the onion halves and garlic and cook over a medium-high heat until the skins char and the onions are caramelized on their cut sides; the garlic should be soft on the inside. Remove both from the pan and set aside until cool enough to handle.
Meanwhile, heat the oil in a pan and lightly sauté the remaining onion until softened. Add the stock and water and bring to a boil. Reduce the heat and simmer for a few minutes.
Peel the charred onion and garlic. Chop coarsely. Add to the soup. Add tomatoes, chili, oregano and cumin. Cook for 15 minutes, stirring occasionally.
Add the citrus rind, season to taste with salt & pepper. Simmer 2 additional minutes. Remove from heat and stir in the lime flesh and citrus juices.
Ladle into soup bowls, garnish with tortilla chips and fresh cilantro. Serve immediately.