Following his defeat (in the first Mortal Kombat game), Shang Tsung begs his master, Shao Kahn, to spare his life. He tells Shao Kahn that the invitation for Mortal Kombat cannot be turned down, and if they hold it in Outworld, the Earthrealm warriors must attend. Kahn agrees to this plan, and restores Tsung's youth. He extends the invitation to Raiden, who gathers his warriors and takes them into Outworld. The tournament is dangerous, as Shao Kahn has the "home field advantage", and an Outworld victory will unbalance the furies and allow Outworld to subsume Earthrealm.

Mortal Kombat II follows Mortal Kombat and precedes Mortal Kombat 3. The story is similar to Mortal Kombat: Shaolin Monks, though some fans argue that the latter has many contradictions to the events in the Mortal Kombat storyline.