Originally Posted by Ninja Ralts
One second...I'll go get my game guide.
Remember the Galactic Warehouse? Inside is a secret entrance to the headquarters. I hope that helps. Also, did you visit all three lakes? If not, do so.
Also, like Team overkill said, follow the grunt in Pastoria until he leads you to the lake entrance's route, where you pummel his Pokemon.
i think that is what you have to do
p.s good luck