>>52380743at least if it's not addressed in the bw2 remakes.
My headcanon is that he disappeared during the Alola crisis.
In the manga, Lusamine was fused with Nihilego for six months, while somehow surviving.
Which led me to believe parts of the rest of the world had to fight the Ultra beasts, but the Submas twins were on a train ready to battle when a wormhole opened up, pulling Ingo in. leaving emmet and the challengers behind. (I'm also writing a PMD origin story where a Xurcitree kills them both)
Anyway, after Emmet's bereavement, he tries to return to the subway, only not to be able to set foot on a train. and that's all the plot details I'll be giving.