What is freedom?

Eliot had prepared himself for this. 

After reading through the mysterious letter, upon understanding the peculiarity of the situation and when deciding to come to this place in person, all that while, all that time, Eliot mentally prepared himself to experience any sort of strange events.

The Church of The Sun was obviously hiding something from him, and for them to be so bold to keep the crown prince in the dark about such a huge project, they must have The Emperor's full support. Knowing that the emperor was probably backing these people, whatever they were doing couldn't be so simple. 

Despite his not wanting to doubt his father, Eliot couldn't cast out the possibility of something nasty going on here. These people could do something without informing the emperor of it. His father wasn't the sort of person to do so many horrible things to his own people or harm them.