The missile launcher is in the east from the location where you disabled the second radar. Its guarded by 8 armed bandits. When you get there check their positions, note, however, that one of them has a device that allows him to detect the Detective Mode. He should be one of the first you eliminate. While securing this location you can use vent shafts, however, listen closely to Arkham Knight's comments, as he may order his men to throw thermobaric grenades into the shaft.
Once you secure the area, approach the missile launcher and hear Batman's comment on its shields.