Enable "?" menu:
Hold Up + Block + Run at the options menu until it shakes

Bonus Galaga-type game:
Fight 100 two player matches consecutively and a game called Land Of Rellim will begin.

Bonus Pong game:
Fight 50 two player matches consecutively.

Stage select:
Highlight Sonya and press Up + Start on the character select screen. The screen will shake and a boom will be heard to confirm correct code entry. You will be able to select a stage after choosing your character.

Random character select:
Highlight Noob Saibot for player one, or Rain for player two, on the character selection screen. Hold Up and press Start. The cursor will select a random character.

Defeating Shao Kahn:
Play a one-player game with Sub-Zero and reach Shao Kahn. When he jumps, press Down/Forward + LP to freeze him in mid-air. Then, get under him and uppercut him. Keep repeating this until you win. Or use Liu Kang and contiually shoot a low fireball until you beat him, it worked for me!

Super endurance mode:
In a single player game, highlight Kano and press Down + Start on the character select screen. The screen will shake and Shao Kahn will say "You'll never win" to confirm correct code entry. Choose your character and select the hardest path. All matches except the first two and the last will be endurance matches. The first match will be against Khameleon, the second match will be against Motaro and the last match will be against Shao Kahn. Some of the endurance matches have at least six opponents to fight in the same match.

Shao Kahn's Lost Treasures:
Select "8-Player Kombat" from the mode select screen and win the contest.

Exploding Babalities:
Perform a babality move. Hold HP + LP + HK + LK when the screen turns black and your opponent turns into a baby. Continue to hold the buttons as the baby turns back into an adult and explodes.

Hidden fatality sounds:
Hold LP on both controllers to hear Shao Kahn say "Crispy" during the Scorpion's Lair fatality. Hold BL on both controllers to hear Dan Forden say "Crispy" during the same fatality. Hold Down during the Deadpool fatality to hear a gurgling sound.

Play with Chameleon

You have to select a ninja ( Scorpion, OLD Sub-Zero, Reptile, Rain, Noob Saibot, Human Smoke or Ermac) and hold down Back + LP + HP until the fight starts then your fighter should explode and becomes Chameleon

Kombat Kodes:
At the Vs. screen, each player's LP, BL, and LK buttons will set the six boxes at the bottom of the screen. Use the following numbers to represent the symbols that will appear in the boxes. The player on the left controls the first three boxes. The player on the right controls the last three boxes. Tap a button to advance one symbol; hold a button to display the previous symbol.

0 = Dragon
1 = MK
2 = Yin-yang
3 = "3"
4 = Question mark
5 = Lightning
6 = Goro
7 = Rayden
8 = Shao Kahn
9 = Skull

Kombat Kode Effect
788-322 Fast uppercut recovery
044-440 No power
300-300 Silent Kombat
100-100 Throwing Disabled
010-010 Throwing Encouraged
020-020 Blocking Disabled
205-205 Winner fights Smoke
769-342 Winner fights Noob
969-141 Winner fights Shao Kahn
033-564 Winner fights Motaro
444-444 Randper Kombat
282-282 No Fear
987-666 Flipper message
550-550 Wavenet UMK3 message
999-999 Version Number message
448-844 "Don't jump at me.."
717-313 Rain is in the Graveyard
122-221 "Skunky!"
004-400 Ed Boon message
987-123 No Powerbars
688-422 Dark fighting
985-125 Psycho kombat
642-468 Play hidden game
788-322 Uppercut Recovery
466-466 Unlimited running
321-789 Super Run Jumps
975-310 Health Recovery
722-722 Combos Disabled
555-556 Special Moves Disabled
024-689 Super Endurance Kombat
484-484 Automatic Kombos
109-901 Bloody Kombat
202-808 "Babalities Are Reversible"
123-321 Winner Fights Khameleon
555-556 Kombat Zone: Kombat Tomb
246-246 Play Pong

For 2-on-2 and 3-on-3:
022-220 Explosive Kombat / Throwing Disable
227-227 Explosive Kombat

Kombat Zones:
330-033 Jade's Desert
666-444 Scorpion's Lair
091-190 Bell Tower
666-333 Graveyard
933-933 Scislac Busorez
880-088 Subway
050-050 Noob's Dorfen
343-343 The Roof
820-028 Pit III
004-700 Kahn's Kave
002-003 River Kombat
600-040 Kombat Temple
079-035 The Street
123-901 The Soul Chamber
077-022 The Bridge
880-220 Kahn's Tower
222-222 Dead Pool
191-191 The Armory
919-919 The Pit
606-606 Star Bridge
101-010 The Tower
007-007 The Portal
166-661 The Pit II
121-121 The Courtyard
212-212 The Wasteland
000-666 The Lair