So what do you think happened to them?
My thoughts. Well...
Perhaps, in the vein of the Jungle Book, his parents were killed in some sort of accident and N (around 4 by my guess) was left in the forest. His ability to communicate with Pokemon helped him get around as a Darmanitan and a Zorua took him in as one of their own. How his parents died and the details are unknown because as N grew up he forgot about his parents and nobody else was there as a witness.
Ghetsis may've heard rumors of a supposed feral child who could speak to Pokemon but mostly kept away from humans. Though much like the Kangaskhan Kid, he'd confront humans who'd hurt his friends like poachers, hence the rumors. The man had a hunch that the boy (now 7/8 years old) was the one he was looking and went to the forest and found him, pretended to be his father. Even going so far as to dye his hair green to make the connection more convincing to the naive lad (other resembling features were pretty coincidental). It didn't take long for the boy, N, to be persuaded into coming with Ghetsis and the rest is history.
What do you think?