Enter the building and reach the place where you need to interact with the hatch in the floor. In the next room, locate the entrance to the ventilation shaft. Go through it so that you are directly below Penguin. Press the appropriate key/button and take Penguin hostage. When interrogating him, you can press the key/button responsible for counterattack in the right moment, but a fight will start anyway.
Good news is that during the battles in this location, you can use Nightwing's help. Just like in the case of Catwoman, you can switch freely between the two characters. Moreover, you should look out for the moment when the game allows you to perform Dual Team Takedown. Together with Nightwing, defeat all the Penguin's thugs.