Stain is exactly what it says. Stain. I am having trouble imagining staining a wood deck midnight blue, and even without the foot prints, your dog's claws will wear scratches and wear patterns on the deck which will be even more obvious with such a dark stain selection.
Varathane or other clear sealers applied over the top of this situation would be difficult to apply correctly, and unlikely to perform appropriately. I would suggest painting the deck at this point, pressure washing the existing deck at low pressure, with an environmentally friendly detergent, rinsing thoroughly, and allow the wood to dry, then applying your exterior latex paint.