The BAD control center is to the far right of Spy island, past Toupee Terrace.
You can only enter the control center when you have rescued all 3 spies and have the Fingerprint from the BAD Bistro.
(see the related question)
spy island
Spy island
The satellite control center
You Get the chameleon from The eye doctor place then put it on then use it in the headquarters.
you click it and move it
on the roof
it's in spy island
The BAD Satellite Control Center is to the right of Toupee Terrace. You need the Ultra Vision Goggles from the third rescued spy in order to see when the lasers turn off. You should also have the Fingerprint from the BAD Bistro on Balding Avenue.
The lasers prevent you from reaching the control center until you get the Laser Goggles from the 3rd rescued spy. (see the related solution question)
It is at the Control Center
You will get a Laser Pen, a "Grappling Bowtie" and Ultra-Vision Goggles to get past the lasers in BAD control center.
In the final building when you are reprogramming the computers. you use the fingerprint to get into the building.