Kung Lao singlehandedly taking out the duo of Shang Tsung and Quan Chi. Keep in mind that in the original timeline, those two mopped up Kung Lao and his companions. Furthermore, Kung Lao bests Kintaro immediately afterwards.
The game actually got awarded best fighting game of the year in an Australian gaming magazine despite being banned there. That's how well-recieved it was.
In the finale, a rejuvenated Raiden channels the power of the Elder Gods and kills Shao Kahn, possibly for good.
Sindel slaughtering most of the heroes without breaking a sweat. Really sets the tone for the finale, a warning that things are going to be VERY different.
Sub-Zero's ladder ending where he and Scorpion join forces to easily defeat the Lin Kuei who murdered both of their families. People have wanted to see something like this for a while, and now they did.