Ok so a few of my ideas are as follows:
For the storyline:
I was thinking along the lines of world domination(as you mentioned in PM Koral) with a bit of a twist.
Maybe it could be more of a government or a weapons research organization thing where they are trying to utilize this 'brain washing' tech to be more efficient so that they can use it on enemy countries, and even their own population to control "rebels of the state".
They could be hiring or forcing scientists that are top in their field to be able to work with the current technology and make it able to brainwash anyone at anytime despite any odd brain chemistry they may have.
They could be releasing some subjects who have so far been declared successfully brainwashed in the field to study it's long term effects in a "normal" environment.
There is still much research and testing that needs to be done because some people either die during the brainwashing process or show an immunity that needs to be exempt if the organization in charge is to use it for nefarious purposes.
((This is an idea to help the scientist characters know a bit more about what they are doing, and for when or if the kids find out what is going on.))
My ideas for the characters:
My scientist character could have his doubts and what not and could eventually rebel against his employers and even maybe help the kids escape under the right conditions.
I was also thinking of having Ella get herself brainwashed later down the line if that was ok.