man I need some help here..lol...I think somone said in a nother post that Sub Zero/noob was from the smoke noob ending so I f I knew how that enede di might have na idea of what the whole story behind that is

People know that the Sub in the 1st game is Noob now because of Noob endings says so. While of course not all endings do happen but a certain key fact such as this doesn't need to happen for it to be true. In this case no matter what happened Sub getting killed or not Noob is current Sub's older brother. Why is MK1's Sub evil? It all began during the time of MK:M Sub Zero. Consider that Sub'Zero was apart of a clan that was killers for hire that is evil. During MKM:Sub Zero goes to the Netherealm. No person can go to the netherealm without having some evil in him. Of course we will never know all the things Sub has done pre events of MKM: Sub-Zero, but 9/10 they were pretty horrible stuff for him to go the the netherealm after Scorpion killed him in MK1. Current Sub of course had to be evil of some sort since he did work for killers, but since then (MK3) he has been fighting for good.
Scorpion is part ( a name I can't 100 remember or spell correctly) is Ryu something. Reptile isn't apart of any clan. He just severs who ever he feels should be a master or a person that that gives him purpose.
Who is in the Lin Kei clan? Well of course pre MK1 through MK4 The clan was a group of ninja killers for hire. Since MK: DA this clan has disbanned. Now the current Sub-Zero(MK2-MK: Deception+ future)) has now taken over with zero members. During the events of MK: DA there was a new member of the Lin Keui. That person was Frost. While still in training she frought along side Sub for a very short time. Since then she died. Currently Sub- Zero is not working much with the Lin Keui clan after Frost has died. He is now more concered about the Dragon King threat. His ending doesn't point to anything doing with the Lin Keui rebuilding saddly.

Scorpion was a member of the Shirai-Ryu before he died at the hands of the original Sub-Zero.

1) Noob is revealed as being the original Sub-Zero in Noob's Deception ending. His soul was tainted with evil when Scorpion killed him in the first tournament. He was transformed into the demon Noob Sabiot apon his entering in the Netherrealm. I personally believe Shinnok had something to do with this after Sub-Zero betrays him in Mythologies. It was a way for him to get his revenge on Classic Sub by turning him into his servant.
2) The Sub-Zero in the game with the new armor is the younger brother. It appears that his medallion has fully healed the scare (in Deadly Alliance it had turned it from red to blue).
3) Scorpion was a member of the Shirai-Ryu Clan. You can read more about their rivalry with the Lin Kui through the Mythologies game as well as Scorpions bio from the first Mortal Kombat game.
4) Reptile does not belong to a ninja clan. He's a part of an extinct reptilian race along with Chameleon. He serves as Shang Tsung's protector under Shao Kahn. He takes the form of a ninja to blend in during the events of the tournament.
5) The Lin Kui members as of Mortal Kombat: Both Sub-Zero's (Classic and Younger), Smoke, Sektor and Cyrax.
As of Mortal Kombat 3: Classic Sub is gone because of his death in Mortal Kombat. Younger Sub leaves as a result of not wanting to be automated.
As of Mortal Kombat 5: Younger Sub takes over the rule of the Lin Kui after defeating Sektor for control of the freeze medallion. Cyrax leaves the Lin Kui and joins the Outworld Investigation agency after they return his soul. This marks the appearance of Frost (which is apparently killed at the end of Deadly Alliance when she tries to take the freeze medallion).
As of Mortal Kombat 6: Smoke is captured by Noob Saibot and reprogrammed to serve him. It's possible that he will join the Lin Kui in Mortal Kombat 7 if he somehow frees himself.

side note: Chameleon (sorry J8son, ur off) was never given a race...Khameleon (the female Chameleon, was made a Zatterean, like Reptile). Chameleon never even had a bio...except that he was Shao Kahn's secret warrior

They are the same character just different palettes for the N64 and the Playstation version. One was male. One was female but only the female character (Chameleon) was given a bio and ending. Therefore she is canon in the storyline.

Chameleon was the MALE ninja that didn't have a story and the other ninja's moves.
Khameleon was the FEMALE character that was given a story and she is a member of Reptile's race.

in that case shujinko is somewhat evil too since he can go to the netherrealm

Oh, thanks for clearing that up. I knew it was one way or another. Truthfully I don't see either of them returning anytime soon (unless they tie it in with Reptiles storyline).