There are a couple I'm having trouble getting, and was wondering if anyone could help.
I have yet to...
Discover a terrible family secret
Make a foreign duke my subject
or
Become an evil minion.
I've gotten everything else!
Checklist items
(Do I really need spoiler tags, based on the nature of this thread?)
Lumen Crystal: Raise Sense Magic before you pass judgment on the man who murdered his wife and blamed it on demons.
Lumen Minister: Again, raise Sense Magic before your ball in front of all the nobles and you should unlock the option.
Sunk a Fleet with Magic: You need at least 3 other Lumens, in addition to yourself, to pull this off. (Once you find the Lumen minister, this should be easier to understand!). Then you pick the option to go out and participate in the naval battle when the Shanjian forces come out.
Lumen Crystal: Raise Sense Magic before you pass judgment on the man who murdered his wife and blamed it on demons.
Lumen Minister: Again, raise Sense Magic before your ball in front of all the nobles and you should unlock the option.
Sunk a Fleet with Magic: You need at least 3 other Lumens, in addition to yourself, to pull this off. (Once you find the Lumen minister, this should be easier to understand!). Then you pick the option to go out and participate in the naval battle when the Shanjian forces come out.
Discover a terrible family secret - This has to do with the Briony subplot.
Made a Foreign Duke your subject - This has to do with Elath and Sedna.
Become an Evil Minion - This is pretty obscure. If Elodie is a Lumen and finds a spare crystal, she can get a conversation with her mentor asking about whether it's possible to combine the crystals. Having had that conversation should unlock an option in the final confrontation with Togami, where you can suggest joining forces instead of fighting. Actually being able to go through with it requires that you've been playing Elodie as evil, otherwise she'll balk.
Made a Foreign Duke your subject - This has to do with Elath and Sedna.
Become an Evil Minion - This is pretty obscure. If Elodie is a Lumen and finds a spare crystal, she can get a conversation with her mentor asking about whether it's possible to combine the crystals. Having had that conversation should unlock an option in the final confrontation with Togami, where you can suggest joining forces instead of fighting. Actually being able to go through with it requires that you've been playing Elodie as evil, otherwise she'll balk.
You might have been a bit evil but that one takes being REALLY evil. 
Hunting while Angry gives you evil points (because you enjoy it in a mean way) and that's grindable. Beyond that, some things you can do:
Throw Julianna into the dungeon.
Punish the maid for bumping into you.
Execute the Duchess of Hellas for starting the war with Ixion.
Execute Banion.
Try to protect yourself against assassins by ordering harsh punishments
Assassinate Arisse.
Execute the Earl of Ishtar for failing to protect Adair
Get Briony killed, then tell her mother that it was her own fault
There are others, but these are some examples of really mean.
If you think you were over the top evil and it still didn't trigger you can send us the log and we can check. We may have made it too hard.
Hunting while Angry gives you evil points (because you enjoy it in a mean way) and that's grindable. Beyond that, some things you can do:
Throw Julianna into the dungeon.
Punish the maid for bumping into you.
Execute the Duchess of Hellas for starting the war with Ixion.
Execute Banion.
Try to protect yourself against assassins by ordering harsh punishments
Assassinate Arisse.
Execute the Earl of Ishtar for failing to protect Adair
Get Briony killed, then tell her mother that it was her own fault
There are others, but these are some examples of really mean.
If you think you were over the top evil and it still didn't trigger you can send us the log and we can check. We may have made it too hard.
