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Well, we think she's a villain, anyway. She's at least the main antagonist of Insurgent. It's hard to tell if Jeanine is a good gal or a bad gal, because her motivations are always clouded in secrecy, and Tori stabs her before she can do the classic "bad guy explains everything at the last minute" speech.
Jeanine is doing brain scans to try to understand why Tris is the way she is—and to get a better understanding of the Divergent. Whatever the results are, we don't really understand them. There's lots of talk about "lateral prefrontal cortexes" (29.87), but we're not totally sure what's up with these fine brain specimens. We have to admit that we kind of wish Jeanine would do more, since she's the only person in this whole book who seems to be trying to understand the Divergent, whatever her motivations are.
Jeanine believes what she's doing is for the good of the city: "It is about keeping this city safe from the people who intend to plunge it into hell!" (33.69). We guess we'll have to read Allegiant to find out. What do you think? Will the city be better or worse off without Jeanine?