Ever since MK2, Shao Khan and Darkseid were plotting to take over the MK and DC realm. So they come up with a plan by creating a portal bridging the MK world and the DC world. So, all the DC characters invade the MK world and believe that the MK characters are the bad guys and vice-versa.

All at the same time, Shang Tsung steals the amulet and revives the Dragon King's army, as he's plotting to use the army to take over all the realms. So then Shao Khan kidnaps Drahmin, holds him hostage and takes him to the Soulnado so Shao Khan and Darkseid can funnel souls into Drahmin and create him into a giant monster who serves Shao Khan and Darkseid.

So as Liu Kang, Kung Lao, Johnny Cage, Sub-Zero, were being awarded by Raiden for protecting earthrealm, a portal opens up and out steps Superman, Batman, Flash, and Green Lantern. They fight, and after the battle they find out that they're on the same side. Then they go find Shao Khan and Darkseid.

When the MK and DC warriors find Shao Khan and Darkseid, they release Drahmin who tries to kill the earthrealm warriors. But then Shao Khan turns on Darkseid and smacks him with his hammer, knocking him out. Then the earthrealm warriors defeat Drahmin and Shao Khan runs away.

Shao Khan runs into the Dragon King's tomb thing only to be ambushed by Shang Tsung. Then he orders all of the Dragon King's army to kill Shao Khan. He tries to kill the Dragon King soldier but Shao Khan fails.

The earthrealm warriors followed Shao Khan and break into the tomb. But Shang Tsung orders the soldiers to kill the earthrealm warriors while he consumes Shao Khan's soul. They kill all the soldiers but it was too late. Shang Tsung absorbed Khan's soul and he becomes super powerful and fights the earthrealm warriors. The warriors defeat him, and Liu Kang does his little flying kick into Shang Tsung, releasing all the souls Shang absorbed. Then Shang dies.

Then all the warriors were awarded for saving earthrealm then the DC warriors go back into their realm.

The end