Police being mind controlled? Hmm... that sounds kinda odd for me.
Anyway, you were clearing the exagerate plant spawn and kicking the ass of that Tangrowth before you took the second gym.
Next, your supposed to do the same. Head to Jesper Ward, the police guy who was blocking the entrance till now, should let you true. He will also tell you all you need to know... If you already did that, then maybe some more precise explanations to where you are might be needed.