Cyber Sub-Zero beating both Goro and Kintaro in a handicap match.
Stryker taking on Reptile, Mileena, Kintaro, and Ermac all in a row and WINNING!
Liu Kang defeating Shao Kahn after the later killed Kung Lao by punching him right through his chest.
Shao Kahn's speech at the intro; atop a pyramid surrounded by the bodies of dead Kombatants, he delivers an extremely Badass Boast as he delivers a No-Holds-Barred Beatdown to Raiden about how he has won, and it marks The End of the World as We Know It. The Call Back at the end of the game suggests he had the speech planned out years in advance, and it shows.
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.