I didn't make it!
I installed the Un-Restored Content Final version mod. There were others I put in there as well, such as the HK Factory mod, Improved AI, and several skins and models.
My problem is that every time I leave the Telos Academy and the Handmaiden comes out, the dialog immediately stops after Atton says "We don't need your help." It goes back to where you control the character, all the others start their normal scripts, and the Ebon Hawk is in this incomplete kind of mode where you can never leave it.
If I have to fix this by fixing the script, so be it, but if there's a simpler fix, please let me know. [EDIT] Also, after reinstalling the entire game and only putting in certain mods again (the ones mentioned), and reloading my save at the Academy, all the other Handmaidens inexplicably turned into golden HK's.