Work your way up Arcade Ladder with all 27 characters including hidden fighters Quan Chi and Cyber Sub-Zero. Set Rounds to 1 in the Options menu and select Beginner after choosing your fighter(s) to make it easier.
If you are struggling to beat the Ladder with a specific character, select Tag Team Ladder and choose the fighter you want the ending for plus your main/favourite character, as this counts as having completed the mode with both characters. You can take advantage of this to speed the achievement up and cut your playthroughs in half.
You can see who you have completed the game with in Nekropolis. If it says "View Ending" then you have completed it with that character.