After the nanobots designed to help humanity begin controlling their hosts, a surviving true human must reprogram the bots, before humanity’s enslaved forever.

I stand corrected.

I guess I spoke out of my rear end there. On the plus side, I learned something new. Maybe Richiev can make use of that as well.

That is a misconception and inaccurate description of the effect of a HEMP (H stands for High-altitude). Because of their extremely small size nano bots would not be affected unless by a strange quirk of fate they fall victims to the phenomena of resonance.
The only people with greater risk are people with metallic hip replacement and other metallic internal prosthetic.
Also nano bots make sense only in huge quantity, that means that the cost of a single unit must be ridiculously low. Also because of the risk of metal poisoning, the nano bots are more likely to be based on electronic polymers. They should not be affected by HEMP and resulting E1, E2 pulse components. Due to the size of electronics, E3 only affect long cables excluding nano bots.

A, sort of, obvious "solution" would be an EMP, Electro Magnetic Pulse. The best known way to achieve this, at the present, is to detonate a thermonuclear warhead in the upper atmosphere (I believe.)

Unless the nano bots are somehow organic, the EMP would render them inert. But there are some problems with this of course. The EMP would also destroy all other electronic equipment in the area it affected. So it would have to be the last ditch attempt to destroy the nano bots. Also, it may not be the easiest thing, or at all possible for the Protagonist to get hold of a nuke and deliver it to the correct altitude and detonate it.

Just a thought, though.