Keep trying until you're Sub-Zero, freeze do 1, 2, 4, change, 3, change, 3, change back to Shotokan, repeat. Same way I beat Kira at the Kochal fight.
Ka-Tra

Personally, I used Jade, and kept pullin off a 10-hit combo w/her. Scorpion never stood a chance. It's really not as hard as everyone makes it sound, and if you still have trouble, crank the difficulty down to easy or novice and try that. Good luck!

MY GOD! THE LAG ON THIS SITE IS TERRIBLE!!!
but anyways, keep trying until you get Nightwolf!
Please read this cause this is the easiest way to beat him and any other character in the konquest missions. I used this technique to beat everyone.
Ok, anyways you start the fight and your nightwolf
STEP 1: Do your foward shadow thing, which leaves a green trail and sends Scorps back
STEP 2:move backward alittle shoot with arrow
continue until you win the match.
This is ultra cheese and the computer falls for it every time.
The only problem is getting Nightwolf, the comp usually picks Lie Mei, Kobra, or Dairou. The CPU must have a hard on for them or something.

I just beat him as Ermac. I spent most of the time ducking his attacks and dodging until he started using his special. As Ermac or Subzero you can take advantage of his special moves as long as you can tell when he's gonna do it. It takes a while to beat him, but you cant just rush at him.

how do you change people?
i got stuck with sindel...shes cool and everything cuz she helped me out in tons of missions, but still i want to know how to get other people...
also, if you beat him, what happens?

you get shujinkos spear move and i used darrius and just used his back, foward square move hit him every time

I used Mileena, and did the cheese thing also. Two of her drop down from the sky kicks, (F,F,4), and then her Sai projectile (D,F,2). Repeat. When you beat Scorpion you get...***spoiler***
Scorpion's spear move for Shujinko.

but how can you change people, though!?
also how do i beat scorpion in nexus?

Yeah, cheese seems to be the popular tactic. I used Baraka. F, F + 3 a lot. (weapon stance) 3, 3, 2, 1, 1 whenever the opportunity arrises.