I agree it does seem out of place. The lyrics in my copy say 'we've reached the highest mountain' rather than 'where is the highest mountain.'
A mountain can represent a challenge. The line could mean that we're standing atop a great challenge. And that while we're not aware, MJ will disappear. Maybe perhaps to work on the challenge? And not to reveal how he did it?
Or I think reaching the highest mountain signifies that he's reached a milestone in his life, after which he would disappear. The rest of the lyrics say 'And together we will fly/We'll dance up in the heavens.' He's suggesting that he can go higher than the mountain- even up into the heavens. Perhaps he's saying that he disappears to work on reaching greater achievements.