Once all conditions had settled down, Professor Runda gave orders to lead everyone in rebuilding the base, while taking along the crystals that Deoxys had been searching for.
As for the Deoxys defeated by Rayquaza, it had transformed into a purple crystal, bearing a striking resemblance to the green crystal the professors were taking with them.
The professors had once attempted to dredge the waters where it fell, but unfortunately, found nothing.
Chapter 19