Story Mode follows the events of the first three Mortal Kombat games but offering a new alternate twist on the saga. There are 16 Chapters that must be completed and 67 fights total. You must follow one character for each Chapter as the story unfolds. You can change the difficulty to Beginner if you go to Options in the main menu.
Johnny Cage (Reptile, Baraka, Sonya Blade, Kano)
Sonya Blade (Sub-Zero, Raiden, Jade/Kitana, Kano)
Scorpion (Kung Lao, Nightwolf, Cyrax/Sektor, Sub-Zero)
Cyrax (Sheeva, Baraka, Johnny Cage, Sektor)
Liu Kang (Ermac, Kitana, Scorpion/Quan Chi, Goro, Shang Tsung)
--End of First Tournament--
Jax (Baraka, Johnny Cage, Jade, Sheeva)
Smoke (Kitana, Kano, Sub-Zero/Reptile, Sektor)
Sub-Zero (Cyrax, Ermac, Reptile, Scorpion)
Kitana (Smoke/Johnny Cage, Jade, Mileena, Shang Tsung)
Jade (Baraka, Sheeva, Mileena, Smoke)
Kung Lao (Noob, Goro, Shang Tsung/Quan Chi, Kintaro)
Liu Kang vs Shao Khan
--End of Second Tournament--
Stryker (Reptile, Mileena, Kintaro, Ermac)
Kabal (Kano, Mileena/Noob, Cyber Sub-Zero, Sheeva)
Cyber Sub-Zero (Sektor, Kintaro/Goro, Ermac, Noob)
Nightwolf (Quan Chi, Cyrax, Sektor, Sindel)
Raiden (Scorpion, Jax-Stryker-Kabal, Kitana-Nightwolf-Kung Lao, Liu Kang, Shao Khan)
When fighting against Shao Khan the first time, hit him with an uppercut whenever he taunts and duck under his spears. Use a low fireball as much as you can to whittle his health down. The second time you fight him teleport behind him and uppercut repeatedly.
You should unlock "Halfway There!" after Kitana's battle with Johnny Cage and Smoke.