There's nothing bar Wish/Miracle, (at least in core), that doesn't allow a save that can deal with CR 28, likewise anything CR 28 or close enough to eb a threat to it has far too many HD for shapechange to allow you to change. Gate/Elemental Swamr e.t.c. are eithier DM resitricted or summon creatures far too weak to be a threat. Likewise without racial silliness and assume every uses the same sort of starting age the best ability modifier to DC is +10, so including core feats you cap out at is 31. if your letting your group exceed that then you inherently breaking what was clearly intended to be the realistic maximum. (IMO Cores biggest issue by far is not laying this kind of stuff out in some kind of guidelines so not just bad hacks would go writing sourcebooks that break them).

Don't get me wrong, 9th levels absolutely break CR appropriate encounters. But if you don't let them move beyond the basic assumptions on things like starting age, race, or DC enhancers core allows they can't scale anywhere close to CR28.