Combine 3 cups water, tomatoes, and chile peppers in a saucepan and bring to a boil. Reduce heat and simmer until softened, about 8 minutes.
Heat remaining 3 cups water in a separate saucepan.
Drain tomato-pepper mixture and transfer to a blender. Blend until sauce is smooth, adding about 1/2 cup hot water if needed. Season with salt.
Cut tortillas into medium chip-sized pieces using kitchen shears.
Heat oil in a heavy-bottomed pot over medium-high heat. Fry tortilla chips in batches until firm and crispy, about 1 minute per batch. Drain on paper towels and let cool.
Spread about 1 teaspoon of the hot oil in a large pan. Carefully pour in tomato-pepper sauce. Add 2 1/2 cups hot water and bring to a simmer. Stir in tortilla chips and reduce heat to medium-low. Stir gently until chips are bright orange but still somewhat crunchy, about 1 minute.
Transfer to serving plates and garnish with onion and queso fresco.
