Step 1: Quan Chi wanted Shinnok's Amulet. It was guarded by four gods he couldn't beat, but he knew Sub-Zero's element could trump theirs.

Step 2: He hires Sub-Zero to steal a map to where the amulet is hidden...but he ALSO hires Scorpion for the same job, knowing that Scorpion's clan is bitter rivals with Sub-Zero's. He does so because he wants to have a backup plan just in case Sub-Zero ever fails and turns on him. Specifically, what he wants is for Scorp to die, so he can use his necromancy to make Scorpion an undead who will owe him a favor, have hellfire powers that can beat Sub-Zero's ice powers, and want to kill Sub-Zero really, really bad.

Step 2 and a half: He pays the Lin Kuei for stealing the map by killing Scorpion's clan for them. This benefits Quan because now he can lie and tell Scorpion that Sub-Zero is the one who killed them, which will piss him off and make him want to kill Sub even more.

Step 3: Sub-Zero eventually DOES turn on him, just like he predicted he would. He sets Scorpion loose and Scorpion kills Subby in MK1.

Step 4: Quan Chi uses his necromancy to make Subby an undead who owes him a favor too, but not the same kind of undead as he did to Scorpion.

Nobody's actually sure WHY Noob Saibot is loyal to the Brotherhood of Shadow after he refused to join them and hated Quan Chi so much when he was alive. All we know is that when he died, Bi-Han's personality changed in some ways. He lost all sense of compassion and he lost all attachment to the things he cared about in life. When he was alive, he knew he was evil and would go to Hell when he died if he didn't change his ways, but he struggled against it, didn't want to accept it. When it finally came true and he lost those things, he decided to embrace it.

It's possible that he's just plain mind controlled, that Quan Chi specifically designed him to be loyal when he brought him back. Noob seems to have free will though, he says he LIKES the way he is and chooses to be that way. It's possible that the only reason he didn't join up with Quan when offered in Mythologies is because he considered them evil and didn't want to help them conquer/destroy the Earth, but when he died and lost his morality and attachments, he just decided to accept being evil and enjoy it, so he finally saw no further reason to say no.

Either way, Quan Chi did it to them so that in the end, he'd end up with two servants. He's pretty good at planning ahead like that...except for the part where when Scorpion inevitably learned the truth and turned on him, he couldn't control or beat him. Seems kinda dumb that he didn't have another one of his backup plans for that.