There isn't much to say about it other than that it's a Japanese ninja clan founded by Takeda, a former Lin Kuei warrior, hundreds of years ago.

Thanks. So he betrayed the Lin Kuei then? (The founder)

Actually, there IS quite much to say...

It is believed that a renegade, Japanese-born Lin Kuei warrior named Takeda developed the art of Ninjutsu hundreds of years ago. He returned to Japan to offer his services and knowledge to various lords and generals during that country's feudal period. Many of his skills and techniques were soon copied and learned throughout his homeland.
The Ninja have never existed as one collected clan. They work as a loosely connected spy network, made up of several small clans. One such clan is known as the Shirai Ryu. Their founder was Takeda himself, making the Shirai Ryu the very first ninja clan. This also made them instant foes of the Lin Kuei and made Takeda a target for assassination. But, he managed to elude his attackers until his elder years, when he died not from vicious battle, but in his sleep - a victim of poison slipped into his tea. Scorpion is the codename for a modern day member of the Shirai Ryu named Hanzo Hasashi.

This is what MKM:SZ tells about that matter.

Takeda left the Lin Kuei and returned to Japan where he became a mercenary, teaching the Lin Kuei's skill and tatics to the highest bidder. After that, the Lin Kuei marked him for death and Takeda went into hiding.

Over the years, the skills Takeda had taught mutated and evolved, becoming the art of Ninjutsu, now any one could learn them despite not have and special skills. Clan's popped up everywhere and the ninja were born.

Takeda evaded the Lin Kuei's assasanation attemps until his later years when finally they had their revenge...not through kombat, but with poison in his tea. By this time the Ninja had become as powerful as the Lin Kuei and were considered their rivals.

Thanks a bunch to all of you.

wait why is sub-zero back on his clan?
didnt he run away because he did not want to be a cyborg or something?

Sub Zero (younger) did quit the Lin Quei clan before MK3 to escape being turned into a cyborg. But between MKG and MKDA, he returned to the clan which had been weakened. Sektor had killed the Grand Master to try and take over himself, but Sub Zero defeated him, which was when he took over as Grand Master and reformed the Lin Quei as a force for good. This is also when he gained the Dragon Medallion.

He also relocated the clan to an ancient temple in a remote location of the frozen Arctic.

BTW: It's Lin Kuei.