[Wave didn't miss a beat, taking a piece of equipment over to the masks and passing it over them, scanning data into the jewel around her neck that slowly glowed as it received data.]

With or without access to an EMP? Your best bet would be to find if Eggman has any global override codes on his machines that you can use to remotely disable them, but knowing him he probably isn't that lazy to have one global code. There's always the smashy-smashy approach, which is probably more your speed.