I have been playing Injustice in my iPad for almost 2 months. Last week I got an update challenge to unlock Scorpion an Mortal Kombat character. I would like to know the link between Scorpion and the DC universe.
Note: Spoilers for Mortal Combat vs DC Universe possible
The link between Mortal Kombat and the DC universe is basically the game Mortal Combat vs DC Universe. However, there is a comic book that is a prequel to the game: Mortal Kombat VS DC Universe: Beginnings.
The story suggests that the Universe of Mortal Kombat began to merge with the DC universe into a world known as "Earth-Mortal Kombat". The merging started with Darkseid and Shao Khan becoming Dark Kahn because of special conditions involving a malfunctioning Boom Tube and Raiden's lightning.
As far as how Scorpion ends up back in the DC universe for Injustice, because reasons.
Also, you can see a list of characters and locations from each Universe can be found here.