When you regain control of Batman, make your way outside. After a long talk, start scanning choppers. Eventually you'll find the one you are looking for. Grapple up to it and steal the command code. From here, head all the way around the city to the Wonder tower. I highly recommend hitching a ride on a chopper when you can because you are pretty safe when attached to one. At Wonder tower, you want to head for the middle level (the one with the two Snipers). Deal with them as you will and then unlock the door there. Head inside.