Here is my idea and characters for MK6. I think that they are quite good and suit the story but please forgive me for lack of detail on some I got bored after a while.

Basic plot:
The sorcerers are dead. Reptile awakes the Dragon King from his sleep. During the official 11th tournament at the Shoalin Temples the Dragon King attacks. He takes hostages (J. Cage, Bo Rai' Cho) to join others, Kitana and Raiden, in his dungeon. He holds the tournament in the Dragon Realm and if the heroes lose the hostages will be turned into his undead warriors.

Characters:
CHAN
For years Liu Kang's younger brother Chan trained to follow in his sibling's footsteps. After Kung-Loa is captured Chan takes his old friend's armor and he travels alone on a quest to fight the Dragon King.

JAX
He and Kenshi are tracking down the Red Dragon in Outworld and the murderer of Sonya and Cyrax but they end up trapped in the forsaken Dragon Realm and forced into the new tournament.

KENSHI
As the new leader of the OIA Kenshi is determined to stop the Red Dragon and help Jax to find the one who killed their comrades in the newest tournament that is being held in the Dragon Realm.

SINDEL
Princess Kitana has been captured by the Dragon King and some say she is dead. Her mother though wishes to travel into the dark Dragon Realm to rescue her by winning the tournament.

FROST
When Sub-Zero left to train with Raiden, Frost was left to control the Lin Kuei. When the old Grandmaster returns to take back what he started she flees into a portal to escape his assassins and ends up in the Dragon Realm.

NITARA
The mysterious Nitara had entered the fifth tournament to find a sacred orb to free her world from Outworld. Now that she has fed on enough beings she is stronger and has joined the Dragon King as her people did thousands of years ago.

BLAZE
Blaze was no match for Reptile's swiftness and by failing to stop him the Dragon King was released. Now the elemental has taken it onto himself to travel into the Dragon Realm to stop the tyrant before he destroys all realms.

DRAHMIN
Once hideous Drahmin's youth was returned after stumbling into the soul chamber with Quan-Chi. Now he is working alongside with the Dragon King to try and open a portal to the Nethrealm.

SAREENA
During Shang-Tsung and Quan-Chi's battles this demon escaped the Nethrealm. After helping Sub-Zero and Frost she was granted access to the Heavens but when entering the holy portal it shifts and sends her to her original home, the Dragon Realm.

DAIROU
It is unknown where this mysterious fighter came from. All that is known is he wears the crest of the Dead Emperor and he has the same uniform as an Outworld warrior but he swears loyalty to the Elder Gods.

BARAKA
Wounded and weakened from previous battles with Quan-Chi, the vicious Baraka returns masked and armored. He fights alongside of Dairou, but what side is he truly on?

ERMAC
Traveling with Dairou and Baraka is the enigma Ermac who once served Outworld. He is just as dangerous as before but he decides to avoid contact with the other warriors and enters the Dragon King's tournament.

SMOKE
For years the cyborg Smoke wandered the Himalayas until his systems shut down. After being found by the Red Dragon they had him reprogrammed to join them and destroy his new targets: the Special Forces and the Lin Kuei.

KIRI
Centuries ago when the Raptors fled from Zaterra to earth this creature managed to prolong her beautiful disguise. After hearing that Reptile has joined forces with the Dragon King she too goes to find a master in the Dragon Realm.

HASHO
This was the man who decided to automate his ninjas thus creating Sektor, Cyrax and Smoke. After falling off a cliff Hasho was said to be dead and the Lin Kuei was disbanded. Now he has returned to take vengeance on the new clan by siding with Mavado's men.

JOHNNY CAGE (secret)
Johnny had finished his recent blockbuster hit "Mortal Kombat: Deadly Alliance" when he heard about the new tournament in China at the Shoalin Temples. Upon arriving with his film crew he is captured by the Dragon King and imprisoned in his dungeon.

BO RAI' CHO (secret)
At the tournament Bo Rai' Cho attended to see his students Kung Loa and Chan Kang compete. When the Dragon King came it was an ambush and Bo Rai' Cho was taken prisoner.

KITANA (secret)
The first realm that the Dragon King attacked was Edenia and by taking Princess Kitana it put the kingdom into panic. Kitana knows that she may die but if she breaks free she will personally kill the Dragon King and his lizard lacky Reptile.

RAIDEN (secret)
Not even the mighty Thunder God was a match for the Dragon King. After Kitana's capture Raiden was ambushed and taken to the Dragon Realm where he was imprisoned and used as major bait to lure the earth warriors to the evil tournament.

SCORPION (secret)
During his battles with the Onis, Scorpion was cast into the soul chamber. When the Dragon King took the last few souls from the soul chamber for his army he took the ninja specter's. Now he is back and after the one who did this to him, Drahmin.

SUB-ZERO (secret)
After the defeat the two sorcerers Sub-Zero was offered the chance to train to become the protector of earth. By learning from Elder Gods he has become very powerful but if he enters the new tournament he will lose his chance at being a god.

SHOA KAHN (secret)
While many did not believe it Shoa Kahn had survived the attack of the sorcerers. By hiding in the wastelands he gathered all those still loyal to him. Now his goal is not Edenia or earth but to have control over the Dragon Army.

REPTILE (secret, sub-boss)
When Reptile stumbled into the Incubation Chamber he cracked the Last Egg and freed the Dragon King. For his services, Reptile was given new powers and transformed into something beyond a normal Raptor, but a Dragon warrior.

DRAGON KING (secret, boss)
Reptile's foolish actions had caused the Dragon King to be released. During the official 11th tournament he attacked earth and took over imprisoning warriors. If nobody can defeat him in the tournament, those warriors and others will join his undead army.