That won't happen.

Sub-Zero is the Grand Master of the Lin Kuei. He works for the good and defends Earth Realm. He has to much obligation to set an example for his students and to the Elder Gods.

Scorpion is a Ninja Specter full of vengance. He is a neutral force turned Champion of the Elder Gods. He does not associate with the living aside from his beef with elder Sub-Zero and his revenge against Quan Chi. Although he has a duty to destroy Onage he travels alone and does not assist either Sub-Zero and Kenshi or Ermac and Lui Kang.

They could hook up but they won't. Most likely do to some resentment towards Scorpion from Sub-Zero for killing his brother. I don't really see Scorpion saving Sub-Zero from Noob Saibot either unless he is under the vow or finds out who Noob is.

You are right, but it would be kind of cool if it did happen

i think it would be cool if Subby turned evil and maybe turn his clan into an evil society as well

I dont think that is possible for Subzero, he is neither evil, or neutral, or whatever it is, he is good. I predict he will never turn evil, unless some spell or order is cast upon him, there is not a chance of him becoming evil.
Scorpion however has a good chance of becoming good, I think so because from evil he turned neutral, so maybe he'll become good.