Either the writer(s) are just giving us a simple mini-series, and an alternate ending. Or they could be teasing a possible return of who could effectively be the series' own version of Wolverine?
WMG / Morphic
We haven't seen the last of the scyther pokemorph.Think about it from a writer's standpoint. Someone creates a character, has that character hyped up to be some kind of major element in the series, only to unceremoniously kill them off at the fanfic equivalent of a first season. Then proceed to make said character the star of their own mini-series, give said character an AU in which they survive, and even tease a possible ship with yet another major character.