Is pizza never taken out of the box and unwrapped safe to bake and eat after several hours?

In my brilliance, (sarcasm), I came home from the store and I set my groceries down and I went to cool down for a couple minutes. Well, a couple minutes turned into several hours. Whoops. Would foodborne illnesses still remain on the pepperoni pizza (the rest of the groceries are non-perishable) after baking if they existed in the first place?