Cover a sheet pan with foil, for easy clean up. Spray or oil the foil so that the nachos will not stick. Spread half the chips on the foil, single layer. Toss half the red onion, jalapeno, tomatoes and cheese; repeat.
Bake the nachos for 15 minutes. Let sit for 5 so that the cheese can set up. Toss the fresh avocado, the chopped cilantro and the red pepper flakes over the top. Top with dollops of sour cream. Sprinkle the salt last.
I make my own chicken often for this, but that is another recipe.