Route 113
By the time the last of your pokemons are healed, a squad of soldiers lands outside the center, and move in to apprehend the Gaia grunts. They ask you what happened, but Nurse Joy is the one giving the most information. With what you went through before, you can piece out what must have happened.
After their attempt at raiding the military base, this group of Gaia grunts ran off after their pokemons got knocked out or injured. They managed to escape from the patrol chasing them, but with their teams so beaten up, they needed to heal.
This Pokemon Center was on their path, but Nurse Joy had already been warned about them. So when the grunts got here, she knew they were criminals, and she was able to lock down the medical system before they could use it. Undeterred, the grunts used their least damaged companions to overwhelm Joy's Chancey, and used a Magneton to scramble communications while they looted any healing items they could find.
They managed to find a some, until they were interrupted by a visiting trainer who managed to escape after his favorite pokemon was knocked out. Not long after, the two of you showed up, and thanks to the warning you were given, you were able to launch a serious assault on them.