Macbook Pro 12,1

Installed linux on usb thumbdrive. Since ive been unable to press anything at boot to invoke choices. When the boot menu appears. Keyboard and mouse are unresponsive. Im assuming the hidden paritions for efi have been messed with. Ive tried repairs, tried internet recovery (froze at 24:00), finally got back into 10.10, then updated to el capitan. Now system runs 100% all diagnostics are great. Boot is the issue. Still freezing, still can choose boot options. How can I wipe the onboard ssd and start again? Or is there a way to simply repair these partitions?

Any and all help appriciated 🙂