For those interested, here's pretty much what goes down.

Story: After all the battles against Outworld forces, Sektor's programming became corrupted and it told him to go destroy the Lin Kuei leader. He did so and the programming told him to take over as leader. But Sub-Zero challenged him for the right and won. Sektor ran off to go start his own clan of cyber ninjas.

Ending: (First shot is a headshot of Sektor) Sektor wandered through Japan and found people willing to go under the cyber-treatment. Using them, he started his own clan (I can't remember what it was called)

(Next shot shows an army of red cyber ninjas standing behind Sektor) The clan spread like a virus throughout Japan and created a state of emergency.