Maybe this is just me thinking too much into things, but in season three, the future they were trying to prevent was one where someone with abilities tore the world in two. Well this episode got me thinking that as Samuel gets his powers amped up when people with abilities are around him, surely (as was in the alternate future) when everyone on the planet has abilities, his powers would be amped up enough to tear the world in two. Could Samuel be the one responsible for that?
Saying that, season three went downhill very fast and there are about 50 different plot threads left hanging from there. I doubt very much if the writers are going to pick up on them and actually give us answers. If i were them i would pretend that the whole thing never happened.