Cipher wasn't dead. True they were disbanded two times by two outliers that managed to get their hands on a snag machine, but that didn't mean it was completely dead. No, they were still there, underground, organizing to take back what was there's. They waited and experimented on the Pokemon they captured, closing their hearts and making them the perfect tools for conquest. And what luck! They found, from other regions, more legendaries they could hope to capture and make them bend to their will.
They watched as they captured one such legendary and closed its heart. Yes, this one would bring them back to their former glory, the ones that stayed thought. But they needed to make sure that no one was watching them, no one was looking for them. They paid close attention to the outside world of Orre, trying to find gaps and closing them. They listened to the news of XD001 being purified and seethed with hate. It was supposed to be unable to be purified, how did they do it? It was back to the drawing board for how to close a Pokemon's heart permanently.
And so they continued their research, hidden from the rest of the world as they plotted to take over the Orre region. And hey, maybe they could try the whole world later.