Possible plot for How to Train Your Dragon 3!
According to the books of How To Train Your Dragon, the dragons vanish but maybe not in a bad way. Since there are so many dragons and since they are all now following Toothless, Hiccup and Toothless have some issues with all the dragons following Toothless everywhere and its causing issues for them and Berk. So in an attempt to find and island for all the dragons so that they can live in peace since Berk is to small, Toothless and Hiccup end up finding a young night fury in the so called perfect island. no other dragons just that one night fury.
the problem begins when some dragons wont go in certain areas or the nests built by the Berks for the dragons are being destroyed. by what looks like Toothless' plasma witch causes issues for Hiccup and Toothless especially since Toothless has been acting weird when they arrive to the island. They could find out that the area they found was the strange land that Drago Bloodfist came from, attacked by night furys possible because one of the night fury eggs where stolen and soled by the towns people aka (Toothless).
Toothless seems to be a very intelligent dragon and very emotional, Toothless' parents or pack leader could have been in raged by this act and destroyed the town and a major war between night furys and Drago Bloodfists people could have broken out, thus killing off his people and most of the night furys, possible even Toothless' father since Hiccup no longer has a father. since Toothless was an egg he doesn't know about this but was probably plucked off a boat from the hoard that first was giving Berk trouble and taken in by the other dragons, BUT he has a home like feeling and often picks up strange sounds and smells.
some how through investigating and having to deal with the following dragons and anger Berk people, they find the nest or safe haven of the night furys and Toothless is reunited with his mother and all is good and well but they all find out soon that the night furys aren't the only ones who survived from the black winged war between the locals.