As promised I'm going to write how this was going to end.
As noted by a few people, this story has gone downhill. Going back to re-write sections of the story would only prove to be painful to everyone involved.
In addition I broke one of my personal rules when it comes to writing to which I'll kick myself for later.
So I will give the general outline to how things go and write out a few scenes that I was going to keep no matter what.
End of the Line
So traveling down the diclonius research facility, Kohta fights his way through much of the security as he frees silpelits. Along the way, he meets Nana and Mariko who fights him under orders by Kakuzawa but were subdued as Kohta continues to travel further down where he frees Kaede from her captivity. Upon facing Kakuzawa, Kohta instills the greatest most terrible punishment the gods ever bestowed on anyone which was being thrown into the void prison (which is the equivalent to Tartarus for the Greeks) which strips a person of all their senses besides their ability to think and feel pain which is meant to torture it's inmate for all time.
Now standing over the hill Kohta, Kaede, and the other silpelits watch as Kohta sinks the island underneath the waves effectively ending Kakuzawa's dream. It's there Kohta kisses Kaede sharing a portion of his magic with her as a way for her to protect herself if her vectors ever fail. Kohta transport the silpelits to a country side area where they can live in peace with the world.
Then some weeks later they meet up with Mayu as they decide to investigate her. In doing so they learn she's an abused child. As Kaede wants to help her, Kohta refuses to do anything much to her anger as she runs off to the girls defense. Of course after a bit of a scuffle, Kohta does get involved. With the matter resolved as Kaede's mother adopts her, Kohta tells Kaede the reason why he couldn't interfere.
"Tell me Kohta" Kaede asked.
The youth could only sigh to this as he walked out to the balcony grabbing the railing as he looked to the night sky. "It's a long story that dates back in a much older time. But simply as it were, a promise amongst the gods was made. A swear upon our word that we would never interfere within the lives of mortals no matter what".
"Why would you all make such a promise? If so, why did you help me then?"
"You're . . . . A special case Kaede-chan. But it's a matter that almost sparked a war between the gods".
Here Kohta reveals Zeus being the ultimate prick that he is used the elves as his personal play things. Odin taking pity on them came to their defense which angered the Greek thunder god. As things boiled between the Greek and Norse gods, things got ever more hectic as other gods started to become argumentative with how they should interact in the mortal world. After a few scuffles here and there, an oath was made never to use their powers on mortals unless under the strictest terms they were being challenged by them or in need to defend themselves. Otherwise everything else was fair play.
Next year then begins at youkai academy as it opens up with Mikagami's pet that Kokoa whacked landing on Kohta. For the rest of the first day, it involves how Kohta and Kaede fills in a few blanks here and there.
A few weeks then pass as the pair are attacked by a witch who is wielding Thor's hammer Mjolnir. In defeating him, Kohta has an emergency meeting with Anna (Amaterasu) who reincarnated into a successful half-Japanese half-European businesswoman and Haru (Sussano) who reincarnated into a simple convenience store clerk. He learns they were also attacked by other witches wielding other lightning based weapons being Zeus master bolt and Raijin thunder clap.
Making sure their treasure tools are safe the trio go to find the shrine they were being kept at was under attack by demons who wanted to possess them. So the trio plus Kaede dispatch them all as the trinity gods reclaim their treasure tools.
It's here that it's foreshadowed that the gods are aware of what Kaede is and that Kohta is playing a dangerous game by keeping her alive. So at this point Kohta tells her if she continues to wish to come along to only use magic and not her vectors.
So splitting up, the trio decides to return the treasure tools back to their owners. But Kohta decides to make a stop in Hong Kong to see an information broker to see if he knows anything about what is going on. Along the way Kohta and Kaede get into a fight with some local gangsters completely crushing them while also being mistaken for Tsukune and Moka. This incident is what initially grabs Fong-Fong attention about going to youkai academy.
Going to Norse territory, Kohta goes to explain to Kaede that Asgard along with Mount Olympus is the last physical remnants of their civilization. Going there they learn that the perpetrator behind the stolen weapons was none other than Loki as he's currently backing fairy tale with resources as he's using them as a stepping stone to reclaim the gods former glory they once had over the world. To work unhindered, he imprisoned his fellow Norse men. So here it's practically an uphill battle just trying to get some sense of order back. It's also here that bits of Kaede's dark side begin reappearing. But eventually they succeed as Odin punishes Loki for breaking his oath as Kaede becomes an honorary member of the Valkryrie. The highest honor beseeched upon a mortal woman.
Celebrating with the Norse gods, they receive news that Zeus had imprisoned Amaterasu for the crime of stealing his master bolt. So making haste, Kohta goes to confront him and explain the situation. But is not believed as Zeus is being an a**hole as he always is. Proving too much, Zeus then takes Kaede from him threatening to have his way with her which gives Kohta the motivation he needed to manage to hurt Zeus. The next conversation more or less goes as such.
"This woman, is she really worth going to war for?"
"As there was Helen of Troy for the Greek, yes" Kohta answered. "For her sake, I will go to war against you to take her back".
Impressed by his bravado, he returns Kaede and offers a deal that if he can pick a great deed he will listen more to what he has to say. So visiting his old friend Apollo, he learns from him that his sister Artemis is currently the gate keeper to the garden that houses the tree of the golden apples. Apollo still goes on to explain how his sister still has distaste for him for something Kohta did in the past hence why her grudge against men. So taking the only route offered, Kaede partly seduces Artemis allowing her entrance to the garden while there she picks the apple.
With some incident or two, it goes more into the background of the god's history. Rather simply the reason they are so ahead of everyone else was because they were the first race on the planet followed by demons then humans. Also the fact that most of the stories about them recorded in mythology were either mortals making up stories about them or not understanding what they saw. But the big thing is that most of them are not brothers or sisters.
With Kaede's complete outbreak of her dark side, it also goes into the reason why the age of the gods ended. The virus that created Kaede was also present centuries ago during the age of the gods. With it, it created beings of unnatural powers with an insatiable appetite for destruction. As these beings rose up to fight the gods, much death occurred until practically nothing was left but ruins and very few of them left to jump start there civilization. Thus there age ended which kick started the age of mortals being the dominant race on the planet.
This starts the first battle between Kohta and Kaede with Kaede's victory almost killing him which ends with Kohta in a coma state due to his unsettled feelings about what he should do.
From here Kaede stealing a great deal of magic starts wreaking havoc all over the world. But to complete her destruction she must first deal with the gods by razing an army to battle them. In doing so, she forcefully recruits all the silpelits and many other malevolent existences long forgotten by humans and demons.
Understanding how dire the situation is, the gods once more take up arms against this threat for the sake of preserving life. Upon the eve of war, Kohta reawakens understanding what must be down. Bringing their powers to bare the gods were off to war against Kaede.
With the use of a little magic, the battle takes place in another dimension in order to reduce the damage done to the Earth. As both sides clash, much death occurs on both sides.
Fighting his way through Kohta, Anna, and Haru barely make it to the enemy stronghold. Somewhat understanding what Kohta is going to do, they give him their items being Sussano sword and Amaterasu tama.
Pushing his way in, the second battle occurs between Kohta and Kaede. As the bout takes place, Kaede is distracting him making him question if he can really take her life while he in return tries to appeal to her to come back to her senses. As this psychological warfare occurs, the battle goes back and forth.
Going all in for a last ditch effort, the two strike at each dealing fatal injuries. This snaps Kaede back to her sanity. However the damage is done. Although Kohta could be saved, Kaede was dying.
Of course he had the option of saving her, but doing so would be far too cruel. When it came to punishment by the gods, it was going to be a fate worse than death. As its then that Kohta makes his choice.
Kohta held her close as Kaede returned the affection while her blood leaked from mouth as her consciousness was wavering in and out.
Holding her tightly, tears began to slide down the sides of his face. "Do you remember all those years ago what I promised you?"
Kaede nodded a bit. "You promised" she breathed out, "you promised you'd always be by my side" as soon she too began to shed tears. Although not in control of her actions, she knew what her darker self had done and there was going to be no forgiveness from the gods for how many she slaughtered. Understanding that Kohta was going to let her die to spare her a life of torture, she also then understood what he was about to do. "Don't" she managed to squeak out biting her lip trying to keep herself steady. "Don't die . . . ."
"It's already done" said Kohta as they were now standing on a spell circle. "I swore I would always be by your side and a god's word is their honor".
"Kohta . . . ." as Kaede closed her eyes as more tears came about.
It is then they die together as the war had ended with Kaede's death freeing the silpelits from her control and others as well.
Finishing things up the god's show mercy to the silpelits. Although dangerous, they were no real threat so long as they couldn't infect others or reproduce. So they were allowed to live out their final days in peace and harmony within the garden of Elysium which was essentially paradise with no sense of pain or suffering there as everything was provided. Receding back into the shadows, the gods resume their normal mortal lives.
Time skip seven years later, Yukari now in her twenties wanders the streets of Kamakura reminiscing the time when she was Kanae and the times she had with her brother and his friend.
A saddened look graced her face. Although she was not Kanae anymore, she still felt the loss of a family member and more so that of a good man. Walking through the neighborhood, the witch soon stumbled out of her daze with someone running into her. Looking down, her eyes widened as she saw a familiar looking boy who was seven years of age rubbing his head after falling to the ground.
"I told you to watch where you were going".
Yukari then looked to the boys female companion equally as stunned due to her extreme familiarity to a girl she once knew except now she had black hair and no horns.
Brushing himself off, the boy stood up while giving a goofy smile. "Sorry miss, I was so excited about today. I was going to show my friend around the park. I'm very sorry that I ran into you like that".
"Geez" the young girl huffed. "You're always trying to show off".
The boy only chuckled in response to this.
Yukari still stunned finally regained her wits as she kneeled before the two children while wearing a warm smile. "You two have been friends for a while?"
"Yep, she likes to get into fights a lot. So I always need to be around her to make sure she doesn't get hurt".
"Don't say it like that. It's not my fault those things happen. They're the ones who usually start it".
The boy chuckled again as he took his companion's hand. "I always promised to be by her side. Someday I'm going to marry her!"
The girl blushed deep red to this. "Idiot . . . ." the girl muttered even though she looked somewhat happy to his declaration.
Yukari chuckled a bit. "You take care of her and make sure to keep her out of trouble OK" as she circled her finger casting a spell on them.
Seeing the sparkles, "what was that?"
"Just a little charm to grant you happiness. Now you better be off now" as the witch stood up.
"Well it was nice talking to you" as the boy then began to run off with his friend in tow.
"It was good meeting you!" as the girl waved before disappearing along with her friend.
Yukari could only warmly smile to this. The spell she casted was that of analysis as she wanted to confirm her suspicion. Receiving confirmation, her smile widened as she watched from the distance as the two kids were happily talking with each other as they walked off. Turning about leaving as well, there was a slight skip to her step. "Perhaps this time around you two can find that happy ending you were looking for" as she was going to watch over them to make sure they reached it.
It's then revealed that Kohta's final spell sent them both to the wheel of reincarnation which completely purified their souls as they were both then reborn back as normal humans this time. It is here that Kohta and Kaede are able to live without the burdens of their past and just live normal lives.
I would like to apologize to everyone reading this as I could not finish the story the way I wanted too.
But for the most I truly hoped everyone enjoyed the ride.