First off, in this game, in order for trainers to take on the Gyms, they have to be endorsed by someone. We also need to talk about a trainer called Bede. He's arrogant, snooty and thinks he's all that. He's also endorsed by the chairman of the league. Anyways, after the fourth gym, he attacks a ruin that the people of the region find to be sacred. After you put a stop to his antics, the chairman arrives, finds out what happened and bans Bede from taking on the Gyms, disqualifying him from the league.
I am in shock and awe with this move in the story line. There are those who get away with a lot of bull crap in previous games and beyond beating them in battle, they are never really punished. Some have a redemption arc, but through it all, they aren't punished it seems.
Here, we get a firm punishment, a very harsh one at that and well deserved. This could get interesting for once. We'll see where it goes.