I think he believed himself and the other augments were the true representation of humanity. He was loyal to the idea of humanity’s continued existence to the better. He just had a really twisted definition of “better”. Still, I would have been more okay with JJ Kahn to be in Section 31 than what was introduced in the Section 31 movie.
I wouldn’t consider jj-Kahn to have any loyalties or concerns for the Federation. He was self-serving and only cared about his other augments.
I think he believed himself and the other augments were the true representation of humanity. He was loyal to the idea of humanity’s continued existence to the better. He just had a really twisted definition of “better”. Still, I would have been more okay with JJ Kahn to be in Section 31 than what was introduced in the Section 31 movie.