Dave's right; a clear finish is just clear, it won't add any significant color.
What you need to do is find a stain that matches, as close as possible, to the original un-faded stain. Apply this to the faded area first, let it dry, then apply another coat to the entire door. Before staining make sure to clean the door and wipe it down with a chemical deglosser, Paso is the best. After the stain dries apply your clear coat.