i have a story line i dont think its the best but with some help an advice who knows

after armageddon taven's 3rd option was to merge the realms.
tavens mistake was paid with his life

10 years later:
the elder gods choose a champion (no idea who)
that champion will be the konquest character
and will try to find the place where the merged kamidogus are
he will travel through the realm with 1 ally (my suggestion is kenshi)
they will travel in MKD style but instead of portals to realms ther will be portals to diffrent places
begin in a prison the champion is freed from a prison by a lightning blast of raiden. raiden is evil but the elder gods forced him to free him
later you will travel through a portal that a soccerer opend the portal leads to a place where you meet kenshi( or anyone else) kenshi wont be playable during konquest but you can spar with him and train with him
you will meet many characters that you will kombat and train with
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but there is a alternative konquest with the force of evil (new threat)
who wants to have the realms merged he'll start in outworld during armageddon his konquest will be to find a way to stop taven but he gets in a fight with a brother hood of shadow hell be injured and dies but when the realms merge he lies in the center of the merging and gain power and his power is a mix between fire and lightning and his konquest will be MKA style in the ending the good and evil meets and battle the evil konquest ends right before the battle the good konquest however will end after they fight since the good has to win
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raiden will be killed in the konquest by fujin raiden wil turn good again and that will be his alternate costume
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lui kang will be a zombie but in konquest you help him retrive human form
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and some characters for example kenshi and champion will be unlocked after konquest and the evil guy too
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when you finish arcade with somone example havik and hel rescurrect shao khan(like in MKD) shao khan would be unlocked so you unlock karacters that way and in konquest and krypt
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krypt koins will be like in MKD and MKDA
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in the ending in konquest the good guy will destroy the kamidogus and through de shattred kamidogus taven will walk out and fight you after that you will unlock taven(tave was the person who was holding the kamidogus merged so when they shatter he will be resccurected)
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side quests will be in konquest
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Characters in the new MK

good champion
evil champion
kenshi
fujin
raiden
lui kang
ermac
reptile
mileena
sindel
shinnok
quan chi
havik
shao khan
shang tsung
scorpion
sub-zero
jade
reiko
kira
ashrah
noob saibot
smoke
sektor
cyrax
baraka
(more suggestions)

SECRET CHARACTERS:
will apear at select screen but you wont know that they exists

in mka noobs ending says that noob and sub zero clashed so a suggest is like a sub-saibot

kano

jhonny cage




lin kuei assasin
shiria ryu assasin



my suggestion

EDIT : on my first post i wrote that the champion should travel through the realms but since the realms is merged it is not possible