I shot down the helicopter at the water treatment facility and detonated the EMP but I can't get any further? What do I need to do at this point to move forward with the game?

There is no EMP bomb at the water treatment level, that's at the end of farallon episode, and to get further at the farallon you need to shoot down both helicopter gun ships then all the guys who are still left, then make it to the evac atop the building.