Whateley Universe/WMG

The person Chou will have to kill is Zhong Lau.
He's an Avatar-5. The Whateley Wiki states that AV-5 describes spirits that really don't need vessels and probably shouldn't be contained. The Dragon could be a major source of upheaval that Chou will need to stop.
 * There's also the flashback Chou had when she was summoned to greet him, of an earlier Handmaid who was going to kill the Emperor. While it's possible the flashback was triggered by the similarity of the situations, it's also possible that Destiny's Wave or one of the Immortals sent her the memory to help prepare her for the similar task.
 * No, Wait. Destiny's Wave isn't going to have her kill anybody. It has had its previous hosts all forced to kill people because, basically, "fate". Well, that "fate" was really just Destiny's Wave steering the world towards it's choice of future, so that when mutants start to appear frequently, they begin a tradition of superheroes and supervillains. Why? So that Destiny's Wave can finally fulfill its dream of being a superhero, of course.

Stormwolf is Hekate's Mentor
Hear me out. Stormwolf is the leader of the Betas, straight as an arrow- and wouldn't it be a great cover if you were one of the bad guys? He's using black magic to shield his mind from anyone who might inadvertently read it or pick up stray thoughts, like Mindbird. Hekate tried to turn him into an insane wolf-creature, but the spell bounced off him- makes sense if he was the one who taught her how to do it. As to how he kept his skills off the records, it's been done before, as Migraine proved. If he pretended to only have the powers on his MID and never showed so much as a hint of magical talent, it could well have been overlooked. (Please note that this WMG came before the author read 'Knife in the Ribs').

Senoir X/Hekate's Mentor is Hank
He's a character that we've seen extensively, but never from his point of view. He's not even a mage. He's close enough to all the main characters to know the details of their lives and plans. He claims to be vulnerable to psionics, but what would be a better cover? He came with a dramatic, but generic backstory which has never been elaborated on. We never see his parents, or anyone else from his history. He's apparently extraordinarily well adjusted compared to, say, anyone else in Poe, and frequently acts in accordance with stereotypes, just as someone who was actually an ancient mage posing as a teenage boy would. He typically acts like a dumb brick, but suddenly becomes a brilliant strategist whenever necessary, and comes up with a brilliant trick or new use for his powers whenever he's about to lose a fight. He even has the access required to place the note for Tansy in the beginning, laying the scene for breaking the Kimbas off from his choice of their friends later on by planting more "evidence". While he never overtly attempts to extend his influence, he just happened to become a security auxiliary, a Grunt, has close ties with STAR league, and has become the official leader of the Kimbas when nobody was looking. Is there anyone else at Whateley that comes close to being this good of a match?

Hekate's Mentor, Nimbus, and Thomas Townsend (Mephisto the Mentalist) are all the same person
If you read "Razzle Dazzle", you will see that pestering several different heros under several different aliases is Mephisto's style.

The reason Stygian is so depressed is because he's alive.
He's Hades, god of the dead- and he's alive. He's longing for his realm, and he's depressed because he's alive and at Whateley, being pulled around by Imperious, instead of being back in the Underworld, ruling the ghosts.
 * Also, he's there, but his beloved Persephone is not. She's still stuck in Hades. Hades, the Underworld, obviously, not Hades the student at Whateley.

Poe's Cottage is an enormous Open Secret
There are geniuses and mind readers and there's a goddamn check box for other orientations and genders on the normal application, Poesies don't act that dumb, and there's a decently higher proportion of Exemplars there. Not to mention, someone could piece it together simply by realizing few to none of the people date outside of that dorm. Gay population is 5 to 7 %, there's no reason to suspect that would change and mutants still have to be trained, regardless of their orientation. An average person could easily pick this up in a month, a genius could probably in a day. What if someone else reads ley lines like Fey, sees pink from all the guys in Poe for instance and recognizes that means gay. There's dozens of reasons there is no goddamn way Poe's can be anything but.

The alternative is that the entire premise is built on something incredibly flimsy and stupid.
 * Fey mentions the gay males having pink tinged ley lines in her first story and lesbians have a steely-bluish. Admittedly that's a bit of Trans Equals Gay but there's plenty of Unfortunate Implications surrounding this series to begin with.
 * Still. The number of ley line seers/manipulators is about two. Besides, perception of the ley lines might vary depending on who's looking. Besides, who's to say that there's no spells or psychic commands preventing people from thinking too hard about Poe?
 * Because then the alternative between lying to people or the premise being stupid is outright mind controlling anyone intelligent or observant enough to pick up on the holes in The Masquerade which is much much worse.

The Team Kimba stories are in-universe fanfiction
Team Kimba are blatant Mary Sues who spout trite sexist dialogue that's overloaded by pop culture. This is because almost all of their stories are in-universe fanfiction. Team Kimba exists in-universe as a legitimate team, but the stories we see on Crystal Hall are someone else's story of "how they met" which has little correspondence with reality.
 * In actual "reality", Poe house really is a psychiatric care dormitory. Much like other houses are designed specifically for students with physically difficult mutations, the Poe house is formed for students with mental conditions. The "real" reason why Team Kimba became a superhero team is because they all bonded during group therapy sessions as they came to terms with a fluid gender identity. They bonded so well that Phase, after reforming his economic empire, funded his more idealistic team-mates and formed a superteam with them.

Grand Mutant Power Unification theory.
All of the mutant powers can be boiled down into three, maybe four main categories: Magic/Avatar, Psi, Warper, and Manifestor(?). All of these powers were once held by one mutant, thought to be the "perfect specimen", called "Specimen Alpha". His/her powers all boiled down to one thing: Analysis, deconstruction, and reconstruction of systems. This was incredibly overpowered and allowed him/her to do anything from read minds, to change the flow of the winds around him/her, to manipulating compounds and atoms. Alpha was immortal and slowly went insane. Eventually, however, he/she decided that insanity and all power was boring and decided to remove him/herself from the universe. Alpha did this by stripping the DNA from his/her cells and releasing them into the world, slowly gaining cells of themselves. Alpha being the perfect creature that he/she was inadvertently gave his/her cells sentience and allowed them to take over the cells of normal humans, turning them into imperfect copies of him/her. The Exemplar gene is not a base subconscious influence, but rather, an attempt to revive the Specimen Alpha into a new generation. The powers that are available now have been severely diluted by the fact that most mutants only have a few of Alpha's cells.

Hekate's Mentor is Fubar.
Fubar is reputed to be the world's most powerful psychic, and he can definitely manifest a form outside his tank- and alter its shape. In addition, he got his present body after encountering something implied to be from the Mythos. Who's to say it didn't corrupt him and give him Mythos magic?