Not everyone in the Pokémon universe is as attentive as we thought. If they can't tell when Team Rocket is in a horrible disguise, then it's no wonder that they didn't notice Ash was really a tomboy. After all, she hid it well.
Ashton is now 16, and one could say she was happy. They would, of course be lying. The truth was she wasn't. Not anymore. It's been a year since her mother unexpectedly passed away and left everything to her only daughter. Ashton was distraught. She wanted to get away, so she ran. Many of her old friends are looking for her (granted they're looking for Ash), with no avail. During this time, a new girl is slowly entering the spotlight. Ashton is back, but not as the tomboy.
With Team Rocket taking over the Indigo Plateau, and with Ashton hiding from her past, will she be able to stand up to Team Rocket and their new, and violent, practices?