This would be my next MK game.

Play as Sub Zero (younger) and Smoke

At the time the Lin Kuei's best ninjas are the original sub zero, sektor and cyrax, with 100% success rates in all assasination attempts

The two are forced to go on several assasination missions through the game as they develop their skills.

Sub-zero and Smoke witnesses the death of the original Sub-zero ninja spectre Scorpion, and the Lin kuei now assign the new Sub Zero to assasinate Shang Tsung. However they realize that the ninja Scorpion (and others) may interfere again and send Smoke as a secret back up to help the younger Sub Zero.

Sub-zero also begins to sense that sonething moves in the shadows...

The two clash with members of the red dragon, black dragon, white lotus, and the special forces.

Smoke's stroyline would be hard to speculate on, as not too much is known about him and dont want to come up with stupid ideas.

The game would end with the begining of the automation sequence in the Lin Kuei and the battle with Sektor and Cryrax which led to the automation of smoke