The timeline of the game has it take place at the end of Mortal Kombat and the beginning to the end of Mortal Kombat II.

Shaolin Monks takes place during the Mortal Kombat II timeline. The opening scene shows Shang Tsung, Goro, and the other evil enemies escaping to Outworld. In pursuit are those warriors from The Order of Light, allies Liu Kang and Kung Lao. After a nearly fatal disaster, the duo make their way to Outworld where the action begins.

The most fascinating aspect of Shaolin Monks appears to be its fighting system. The game makes interesting use of analog stick in a control scheme with infinite combos. The analog stick lets you control the direction of the attack, the face buttons select the type of attack, and the shoulder buttons modify the attack selection. Attacks can be linked together, allowing you to nail single enemies with a barrage of blows or bash multiple opponents in one chain. The Shaolin Monks' system is quite different from those games of the past, in that it uses the analog sticks to select direction rather than executing just the attack.

Liu Kang and Kung Lao are protagonists of the game. The storyline fills in a lot of the gaps and addresses some of the rumors circulating about the Mortal Kombat series. In addition to Liu Kang and Kung Lao, there are characters for you to unlock. Several characters appear in cameo and/or helper roles, including Johnny Cage and Raiden. Numerous villains appear in boss fights, including Goro, Reptile, Ermac, Mileena, Kitana, Jade, and Baraka. There is a lot of interactivity within the game, and, instead of mere fighting, enemies serve other purposes as well. You can use them as a human shield, run off them to propel yourself to another enemy, and throw them through walls to unlock secret passages.

The  storyline of Mortal Kombat: Shaolin Monks follows the basic story line of Mortal Kombat II from 1993 (regarded as one of the best Mortal Kombat games of all time). However, being only the second Mortal Kombat game at the time it came out, there was not a huge ability to tell a deep story. In Shaolin Monks, they got into a lot more details of the story than they could originally. The game opens with a big opening movie that is the final battle of the first Mortal Kombat tournament. The levels and areas of the game are based around the original backgrounds of Mortal Kombat II. For example, the Living Forest was a small 2D stage, but in Shaolin Monks it is a fully interactive 3D level with many areas.

Liu Kang and Kung Lao are the two characters the story centers around in this game. The player will go though the realms and interact with a lot of different Mortal Kombat characters. In the Wu Shi Academy, the player works alongside Johnny Cage to defeat the enemies. Later the player faces Baraka in a boss battle. As the player progresses, they can unlock two other playable characters for the adventure game. One of the characters is Sub-Zero, and the other character will be Scorpion . Alongside those two, four known characters in the versus mode will be Reptile, Kitana, Baraka, and Johnny Cage.

Mortal Kombat: Shaolin Monks has a gameplay device called the Multi-Direction Fighting Engine. This engine allows the player to deal with many enemies at one time, fight in any direction at any time, and link combos in any direction the player chooses. Also, the engine allows the player to launch an enemy into the air and follow them into the air and continue their combos. The player decides when to toss an enemy into the air or attempt to throw them, and then once the enemy is in the air the player can choose to follow them up into the air and continue to fight them or choose to turn their attention to another enemy while continuing their combo. Also included is a co-op mode wherein the player and a friend can team up and work together to get through the game. There will be areas and items that will only be accessible via co-op gameplay. Also, there are specific team moves and combos the players can only do while playing in co-op mode.

No Mortal Kombat game would be complete without Fatalities. Included are some old school Fatalities that get some updates with new technology in the 3D world. There are also some more new Fatalities for the characters to give the players variety in regards to the disappointing one-Fatality per character in Deadly Alliance. The player can unlock the ability to do Multalities, which is a fatality performed on multiple enemies at one time. Brutalities from Ultimate Mortal Kombat 3 have also been brought back and upgraded to the 3D world.

A good contribution to this game is the unlockable version of Mortal Kombat II, whilst not the complete original verson of the game (there are no difficulty differences, and fatalities are either different, or some do not work), opening this is not difficult, all that has to be done is complete the 5 missions given to you by Smoke in a hidden section of the living forest and is accessed in the main menu's Kontent screen. (note: although Smoke's missions are available in the European release, Mortal Kombat II is not unlockable)

Throughout this game are coded messages written vertically, translateable through the references of Concept 86 and 87, unlockable pieces of Concept Art via Ko-Op, exclusively. The text on the tournament victories wall in the Portal (later leading to the Foundry) reads "LIU KANG WILL DIE", obviously referencing (though technically predicting) Liu Kang's death during Mortal Kombat: Deadly Alliance. Several banners surrounding and en-route to Mileena's arena in the Living Forest treetop area read "TOASTY" once translated. Two glowing symbols above the entrances to the alternate routes in the Soul Tombs read "FIRE" and "WIND", respectively. The symbol for "LIZARD" is repeated several times within Reptile's Lair in the Living Forest, most noteably as the activator of the statue challenges.

The game had received enthusiastic reviews from critics and gamers alike, especially in comparison with the previous two spin-offs (Mortal Kombat Mythologies: Sub-Zero and Mortal Kombat: Special Forces), which were critical and commercial failures. Among the game's strongest points include its efficient and simple gameplay and a likeable soundtrack-- many songs are actually re-mixes of Mortal Kombat I and II tracks, as well as having a large arsenal of gruesome finishing moves that can be performed at almost any time.

Unlike Mythologies and Special Forces, which were prequels to the original Mortal Kombat, this one takes place between the first and second games, which gives experienced players a sense of nostalgia as the game shows familiar sights like the two Pits, the Kombat Tomb, the Living Forest, the Tower, and the Portal.

Some reviewers were right about glitches in the game. The PS2 version had few clipping problems for the enemies and causes the game to slow down, the only way to stop it is to defeat the enemy that's halfway through a wall. The Xbox version has similar issues but also experience points that goes up by itself at random times. The Xbox version does have a rare glitch were the map appears to show a series of slanted ones and "/" marks down many rows for a split second.

However it does face much criticism for its storyline. Many feel it completely ignored/changed the majority of the events of Mortal Kombat II (ex. Kitana being under a spell, Scorpion trying to kill Liu Kang and Kung Lao for no reason, Goro being killed by Johnny Cage in the game though it stated in MK II that he was killed during the original Mortal Kombat Tournament), and many feel flabbergasted that even with a person hired to write the script and check for continuity between games that many events were retconned. Many, especially long-time fans and storyline enthusiasts, regard its story as a what-if tale, although this may be for moot: it seems implied by the makers of the game and series that this game is to be considered canon and replace Mortal Kombat II in the timeline.

Differences between this game's storyline and Mortal Kombat 2's storyline

The basic premiese of the plot is completely different. While Mortal Kombat 2's story was only told through bios and endings, it's clear that a lot of things have been changed. The official Mortal Kombat 2 comic book was believed to be canon since it was written by John Tobias himself.

1. Kung Lao being there at Shang Tsung's island. Kung Lao's original story was that he did not want to be the Champion of Mortal Kombat and was more of a quiet, brooding, reluctant hero, who only fought when he had to. Here Kung Lao is depicted as being an arrogant jerk who resents Liu Kang for winning the Mortal Kombat Tournament and desires to be Champion himself.

2. Liu Kang was not present when the Tarkatas attacked the Shaolin Temple, his MK2 bio made this very clear. In this game, he is present and helps fight off the Tarkata.

3. Johnny Cage is said to disappear from the set of his latest Hollywood Movie (assumed to be the first Mortal Kombat movie), instead he goes to the Shaolin Temples and follows Liu Kang there. (Though it was never said, it is most likely that he was told by Raiden of what was happening and joined Liu Kang and followed him there)

4. Raiden is said to warn the Earthrealm Warriors of what is happening, but also according to his MK2 bio, he disappears after doing so, believed to have ventured into Outworld alone. Here, Raiden (although actually a disguised Shang Tsung, but still nonetheless a change.) guides Liu Kang and Kung Lao through Outworld, thus the Raiden disappearing is never known until the end of the game when originally, all of the Earthrealm Warriors knew that Raiden had disappeared.

5. The final battle in MK1 goes about differently, according to the MK2 comic, after Liu Kang defeated Goro, thus becoming the new champion of Mortal Kombat, Shang Tsung challenged Liu Kang to Mortal Kombat, forcing all the other fighters into an alliance. Kano, Sonya and Johnny Cage foguht an enraged Goro at the Pit while Raiden along with Scorpion and Sub-Zero fought Shang Tsung's army on the beach. After Liu Kang defeats Shang Tsung, the island DOES begin to crumble. Liu Kang escapes somehow on his own. Scorpion fights with Sub-Zero, killing him and then turns to ash. At the Pit, the bridge breaks and Goro, Sonya and Kano all fall to their apparent deaths while Johnny Cage grabs onto what's left of it. Raiden saves Johnny Cage, who gets him off the island just in time. Here in Shaolin Monks, the fighters are all at Shang Tsung's palace fighting one another, which was never explained as to what led up to this event. (Scorpion vs. Sub-Zero, Sonya vs. Kano, Johnny Cage vs. Reptile), no mention is given to Liu Kang defeating Goro. Here Kung Lao, who was disguised as a Masked Guard saves Liu Kang when Shang Tsung tries to devour his soul and fights with Baraka, who was never confirmed to be at the tournament either. What is left intact is that Liu Kang defeats Shang Tsung with his Flying Kick. However Goro then comes out and then attacks all the Earth Warriors, stunning them all. Shang Tsung opens a portal to escape; Goro, Kano, Baraka, Reptile and most strangely among fans, Scorpion follow him through. It begs the question as to how Scorpion could've gotten back to kill Sub-Zero or why you see Reptile on the Pit bridge later on.

6. Shang Tsung's youth restoral is changed. In his MK2 bio, it is stated that Shao Kahn was the one who gave Shang Tsung his youth back which set MK2's story into motion. Here he gets his youth back from the Soul Tombs.

7. Aside from a brief mention of the character, there is no reference to the impending Sindel resurrection in Mortal Kombat 3, in fact it is implied that Mortal Kombat 3 does take place at all.

8. There is no real tournament in Mortal Kombat: Shaolin Monks. Instead it is mostly Liu Kang and Kung Lao running around and defeating the Outworld fighters. Johnny Cage, Jax, Scorpion and Sub-Zero are meant to participate in the tournament as well.

9. There is no mention of Sub-Zero's mission to complete his brother's failed assignment to assassinate Shang Tsung. Instead it is implied that his Mortal Kombat 3 story is taking place at the time.

10. Goro is not thought to be dead after MK1, nor does it seem he goes into exile, since Kitana and Mileena know where he is. Goro is not supposed to reemerge until Mortal Kombat 4.

11. Sub-Zero knowing that Noob Saibot is his brother: in Noob-Smoke's MK:D ending, it is mentioned that neither have seen each other since before Noob Saibot became a wraith.

12. Quan Chi getting the amulet at the end of the game spurred a huge controversy amongs fans of the series. For Quan Chi is believed to have had it since the end of Mortal Kombat Mythologies: Sub-Zero. Here, it is rather strange that Shao Kahn has it and Quan Chi gets it from him.