I feel like I'm missing info (or forgetting). Let me see if I got my facts straight and you guys can either add or correct me if I'm wrong (I'll try to divide it by sections):
That's a lot. I'll make an effort to answer a few.
A. History/Plot:
1. The 2000 soldiers were all Lucius.
3. The Council is Dexter, Xanthe, and the Captains.
B. Secret Stuff:
3. Deus could absolutely have figured that out through future sight. It's OP.
C. Ella:
2. Orang Minyak, to be specific.
4. Deryl was not intended to replace you, he has a more specific role. The role that MC and the others fill is a "host" for something. So it might not be a good thing for us.
6. Charlie has been searching for her brother, this is later revealed to be Oscar Leicht, the big Red Light Green Light guy, who is dead, his corpse kept by H.E.R.O. after his demise.
7. Ella made Jake a Superhuman in order to have him fill the same role as you- but conveniently, Jake can also mind control Deryl, as a way to have undying loyalty for him to become a Superhuman and repair a Heart.
9. Ella's Evolution wasn't exactly what she wanted, as she is "really not the one, after all."
She then talks to someone or something that is speaking with her mentally.
"Quiet, I don't answer to you. Stay out of my head."
"We do things my way."
"Just go to sleep like everyone else, I'll handle it."
Could be indicative of a Memory-based power, but entirely uncertain.
12. Ella wants you to succeed for whatever purpose she has, presumably to host... something.
D. Superhumans:
1. You have 2 parent monsters.
The 3rd, Body, and the 4th, Memory. Both are capable of memory and body-based powers, but presumably more skilled in the use of their namesakes. The one who infected you is the one other monsters note as your progenitor- and can be considered primary. WW has stated this won't change too much.
2. Ella has 2 parent monsters, the 3rd, Body, and the 4th, Memory. Her primary parent is the 3rd, Body, and she primarily manifests Body powers, and so far the only thing she has shown that might be Memory-related is her Sight.
3. Alice has 1 monster parent, the pixie you find during the Mafia plotline (alive); ability to manipulate certain forms of gravity.
4. Michael has 1 monster parent, the 2nd (alive). The Leigong, the lightning monster, was destroyed, and is not his progenitor.
The 2nd has powers relating to energy, broadly. We do not know its name. We do know it is the Leigong's primary progenitor (58%).
5. Danica has 1 monster parent, the cross monster (M65-Gestas)(alive); ability to "mark" enemies with a lethal cross in various ways.
7. Charlie has 1 monster parent, unknown (unknown); ability to set conditions/rules on a target but is limited to three, the third of which requires an oath.
9. Zach has 1 monster parent (presumably), unknown (unknown); ability over time? Is noted as Xanthe's ace before Deus came along. -Codename Kronos. Definitely related to time.
-Might shares a progenitor somewhere along the line with Deus, who I personally guess is a more "pure" spawn.
E. Monsters:
3. There are 12 "Numbered" with broad, conceptual abilities, which are ranked by age as the original monsters which all lower monsters branch off from in accordance to ability similarities.
4. Half of the Numbered Lords, 7-12, are different in an unspecified way.
5. Minyaks are a subspecies of the extinct Orang-Minyak, and their male victims presumably turn into Orang-Minyak.
6. They'll come from the moon...
7. Kenny, and Bailey refer to their parent Minyak as Mother, because it is their monster progenitor.
In the same manner, MC refers to the 4th as Mother or the 3rd as Father during his evolution.
8. Monster corpses can have their abilities repurposed by Xanthe.
10. You receive various dreams with high corruption, but whether they are from the 3rd/4th is unknown.
The dreams are the same regardless of the parent.
12. Valravn was a raven turned into a monster intentionally by the 7th, Lord of Dark. Which he valiantly serves even now.
F. Dead Ends:
1. Ella kills you if you reveal too much of your potential, she then leads you to 4th, Memory, for an unknown purpose.
Before her intentions are revealed, the 7th, Lord of Dark, destroys the 4th's avatar. This was NOT what Ella expected, Ella presumably dies offscreen, frozen in fear, and it DEFINITELY kills you.
3. The jellyfish venom, and the explanation MC gives, reveals that he has "inherited both traits, with the perfect amount of mutation." He is "already perfect." She was looking for the Memory trait. The one she lacks.
I made a mess of this and didn't stick to a format. Didn't answer everything, but hope what I did helps.