The dragon's somehow catch a disease, only dragon's can get. There are eggs from almost all of the dragons, and since everyone knows that it takes centuries for dragon eggs to hatch, Hiccup, Astrid, and the gang hide the eggs after the dragon's have disappeared. When Hiccup is looking back to his youth he remembers the eggs. At the very end of the movie, the last scene is an egg. Before the screen goes black, it starts to glow night furry blue, and a small crack forms in on spot.