A young man named Shujinko is tricked into spending his life collecting the Kamidogu for Onaga, who uses the guise of an Elder God. This is, strangely enough, prior to Onaga's resurrection in the body of Reptile. Onaga only reveals his identity and intentions after Shujinko has gathered the Kamidogu.

In the final events of Deadly Alliance, Raiden's warriors lay defeated during their battle against the Tarkatan warriors and ultimately, the Deadly Alliance itself. The Elder Gods had advised Raiden not to interfere, but he defied their wishes; alone he challenged the alliance of Tsung and Quan Chi inside Shang Tsung's palace, in Mortal Kombat. He had the upper hand for most of the fight, besting Tsung and Quan Chi, until Tsung absorbed a soul from the Soulnado and knocked him down with a fireball. From there, Quan Chi and Tsung combined their powers to defeat Raiden, with Quan Chi levtating the helpless Thunder God and Tsung using a fireball to strike Raiden down.

With Raiden defeated, the Deadly Alliance turned on each other, with Tsung wanting Quan Chi's amulet. The Deadly Alliance was no more and Tsung found himself facing his one time partner Quan Chi. Despite Tsung's efforts, Quan Chi proved too much for him. When Quan Chi stood alone, a hulking form entered the tomb, and the mummies of the Dragon King's army turned to kneel. In disbelief, Quan Chi looked in shock and in great horror... Onaga, the Dragon King, had returned.

Quan Chi knew what the Dragon King had come for: his amulet. Quan Chi used his powers against Onaga, but he could not stop him. Even with Tsung, and then Raiden, helping him, they could not stop Onaga. Raiden concentrated his godlike essence into a single blast, which destroyed the palace and everything within, but Onaga was unharmed, and possessed the amulet.

Onaga now seeks to use six artifacts called Kamidogu to fuse the realms into the One Being, resulting in the destruction of everything therein. Those fighters not killed in the battle against the Deadly Alliance must now stand against him and his supporters. These include the Tarkatan horde and their former allies, who were resurrected by Onaga and are under his control.

Due mostly to the inclusion of several cameos in Konquest mode (as well as in the Dark Prison arena), Mortal Kombat: Deception features nearly every single character from the Mortal Kombat series in some form or another, ranging from the well-established (Liu Kang, Sub-Zero, etc.) to the more obscure (Rain, who is a non-playable character in Konquest mode).

Mortal Kombat: Deception is the first Mortal Kombat game to feature Stage Fatalities (now known as Death Traps) since Mortal Kombat 4. Since then, Stage Fatalities were not seen. The re-introduction of death traps into Deception makes the game far superior in this aspect than its predecessor Mortal Kombat: Deadly Alliance (which featured only one fatality and no stage fatalities).

New Characters such as Dairou, Kobra, Kira, Ashrah and others all make their official debut in Deception.

Is the first Mortal Kombat game to feature two "human" characters as a sub-boss rather than the traditional hideous creatures such as the Shokans, Centaurans or Oni. The new sub-boss (so to speak) is the tag-team tandem known as Noob-Smoke.

It is rumored that such stages like the Dead Pool and the Living Forest were brought back due to fan complaints as they were popular stages in the Mortal Kombat series. The same complaints were also rumored to be responsible for the reappearance of both Raiden and Liu Kang, who were originally slated to make no appearances in Deception.

Kitana was supposed to be featured in this game. However, it was decided that the storyline would change and have her dead in favor of the reappearance of Jade, who has not been featured in many Mortal Kombat games.

Some characters (such as Darrius for example) are said to be plays on established Mortal Kombat characters. Darrius, in this sense is said to be a play on Jax, who was the first Mortal Kombat character of different colored skin. Other characters such as Kira and Kobra are actually hybrids of different characters such as Sonya Blade, Johnny Cage and Kano. Kira, for instance, has Sonya's and Kano's special abilities (plus a fireball of her own, presumably a play on Tanya's fireball in Mortal Kombat 4) while Kobra's moves are identical to the ones Johnny Cage used in Mortal Kombat: Deadly Alliance.

Although the deceased Earthrealm warriors from Deadly Allaince (Jax, Sonya Blade, Kitana, Johnny Cage & Kung Lao) are stated to be under the Dragon King's control after he ressurected them, the characters are not playable. The only character that has died in the Deadly Alliance/Deception story and returned as a playable character, was Liu Kang. The deceased Earthrealm warriors, with the addition of Quan Chi and Shang Tsung, are fightable in Konquest, in fact some have to be fought to unlock other secrets (for example, you must fight Jax to unlock the temple in which you find Liu Kang's training). All of them use other characters' fighting styles except Jax, who, surprisingly, has a completely different set of fighting stances, the prominent of which is Muay Thai, and uses a set of Tonfa much like the ones used by Talim of Soul Calibur II. He is the only non-playable character besides Onaga to have a completely different fighting style.

MK:D's stages are highly interactive, with multiple levels, breakable boundaries, and instant-death traps. Characters can no longer be slammed against walls (visible or not), however.

MK:D also has a "Combo Breaker" system which allows players to interrupt combos up to three times per match. This is generally regarded as a welcome change to Deadly Alliance's uninterruptible combos (combos tend to be shorter in this game as well).

Weapon impalements are no longer in the game, due to the introduction of death traps.

MK:D's characters have two Fatalities and a Hara-kiri suicide move.

Characters are more specialized as well, boasting unique (though sometimes held over from Deadly Alliance) throws, finishing poses, and rises after losing one round (e.g., Sub-Zero shoots ice to the floor to lift himself up, etc.). Also, perhaps due to complaints, every non-weapon fighting style includes an uppercut, a trademark of the numbered series (1 through 4), but used only sporadically throughout Deadly Alliance.

Certain stages also contain their own unique stage weapons often following the stage's theme, that any character can pick up and use.

Other than the above notes, gameplay remains virtually identical to that in Mortal Kombat: Deadly Alliance.

MK:D's Konquest Mode allows the player to play Shujinko in an RPG-style format (but with normal Mortal Kombat battles). Konquest mode reveals a great deal of the Mortal Kombat universe's history.

MK:D's Krypt is smaller than Deadly Alliance's (400 Koffins as opposed to 676). This reduces the number of "filler" Koffins.

MK:D adds Chess Kombat and Puzzle Kombat game modes. Chess Kombat is similar to classical chess, but uses player-selected characters as pieces, and pieces must engage in Kombat to take a piece (much like the 1980s computer game Archon). Puzzle Kombat is reminiscient of Super Puzzle Fighter II Turbo, a puzzle game by Capcom.

MK:D does not contain the Test Your Might or Test Your Sight minigames.

MK:D continues the dark theme, starting off with a whimper for the forces of good and getting worse. It is the first game in the series to assume that the good guys lost the battle of the previous game.

The character Noob-Smoke switches character models instead of fighting styles (Noob fights with Monkey style, Smoke with Mit Zu). They are playable after unlocking, and appear in Arcade Mode as sub-bosses. (Note: in the GameCube version, Noob-Smoke is playable without unlocking.)