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Mortal Kombat Armageddon: The Elder Gods are warned in advance about a coming apocalypse should the titular tournament continue to be held, yet instead of shutting it down pronto, they hand the problem off to a lowly protector god, who comes up with an inane Gambit Roulette involving his two sons, a firespawn created by his wife, two items of war, and a pyramid, which will only be set in motion when the events causing Armageddon have already started. Johnny Cage is the next messiah for the good guys. Raiden joins forces with the bad guys to ensure the safety of Earth, and resurrected Liu Kang's corpse as his enforcer. Jarek is now obsessed with perfecting his Fatality techniques. The Elder Gods screw over Scorpion after he served as their champion. Several characters grow to disproportionate size or become Body Horrors when they absorb godlike power during their ending. None of the loose plot threads of the series are resolved. And to top it all of, the new protagonist's ending - the one that will most likely be treated as canon in the next game - has the Gambit Roulettefail, instead exacerbating Armageddon rather than preventing it. You can't possibly enjoy the game for its story...
It gets worse if you listened to Ed Boon, creator and SCRIPT WRITER talking about how it's "Armageddon" and "Most of the characters will die, leave, or have their stories wrapped up" only to have the game do NONE OF THOSE THINGS!
Well, the canon ending to Armageddondoesn't have Argus's overly complex plan fail due to Blaze's corruption. Instead, it fails because Taven doesn't fucking win the race to the top of the Pyramid. Everyone is killed, and the one left standing is Shao Kahn. So, the ludicrously inept plan ended up backfiring ridiculously, giving supreme power to one of the main villains (if not the main villain) of the franchise.
Mortal Kombat: Shaolin Monks is even worse, with a complete butchering of the storyline for Mortal Kombat II: Kung Lao is now an aggressive and jealous punk instead of the pacifist he was in the games; Kabal somehow appears in Outworld for no real reason; Liu and Kung Lao accept Shang Tsung/Raiden's demand to keep killing in Outworld to "weaken" Shang Tsung with little argument, despite knowing that the sorcerer grows stronger the more souls he consumes, essentially having their slaughter making him stronger, Kitana being under a spell; Shao Kahn given little acknowledgment until the very end (even though he was the main villain from MKII onward); and Quan Chi is seen, in full Deadly Alliance gear, including glyph tattoos, picking up Shinnok's amulet off of Kahn's corpse (even though MK4 and Mortal Kombat Mythologies Sub Zero have already established that he's had the real amulet - and the fake one being still held in the Temple of Elements - for the entirety of the first three games). "Alternate retelling" be damned, this is pure They Just Didn't Care at its worst.
Mortal Kombat 9's story mode has continued the fine tradition of the games above in terms of WTFery;
Several things in the timeline change independently of Raiden's actions post-visions, namely several MK2 and newer characters such as Smoke, Sector/Cyrax, and Nightwolf appearing in the original game's tournament, and Mileena being made by Shang Tsung during the events of MK2 instead of long ago. Yeah, sure, we expected some things to change due to Raiden's attempt to Set Right What Once Went Wrong, but there's a difference between characters winding up in the wrong place due to Raiden telling them to do so, and them being there because the plot says so.
Sindel's No-Holds-Barred Beatdown. The characters she defeated were much stronger than her, especially Sub-Zero (Kuai Liang), whom he defeated both Kintaro and Goro simlutaneously. You might think their combined force could defeat her, well, guess what, she defeats all of them with less-than-minimal effort in seconds. Sure she's empowered by Shang Tsung's soul, which would make her an interesting boss on par with them but the fact that there was no foreshadowing and that the characters she defeated all of a sudden were stuck by a heat-seeking, precision-guided, extra-sticky Idiot Ball took it too far for most fans' standards.
Worse is that Sindel being empowered with Shang Tsung's soul by Shao Kahn was caused by Raiden killing Motaro in an attempt to save Johnny Cage, effectively rendering him an Unwitting Instigator of Doom.
The Elder Gods claim that they can't do anything to punish Shao Kahn's invasion of Earthrealm until he fully merges it with Outworld, stating that it's the merger without an MK victory that breaks the rules, and not the invasion without a victory, in and of itself. This is patently stupid, as that's like saying that the police can't arrest someone for breaking into your home unless they stole everything in it, as well. Furthermore, if the invasion doesn't break the rules but their merger does, what's to stop Kahn from holding off the merger until he's taken over the Earth, subjugated its people, and forced Earth to throw the next ten MK tournaments to win the right to merge them "fairly"? No wonder Sindel and Quan Chi both agree that the tournament is a waste of time and the Elder Gods are ineffectual dicks.
However, the intention of the punishment is not to protect Earthrealm, it is to prevent the realms being merged, which is implied to release the One Being.
Then they should punish any interrealm invasion to ensure that people know better than even attempt such a thing instead of making a tournament and allowing the possibility of realms merging to even exist.
In order to save Earthrealm from Kahn's invasion, after the Elder Gods tell him to fuck off, Raiden makes a Deal with the Devil with Quan Chi, offering his soul and those of all of the fallen warriors for his help in stopping the invasion. Note that, according to the leak, Mortal Kombat Mythologies Sub Zero is not among the events in the series that is altered in this game, meaning that Raiden still allied himself with Sub-Zero the Elder to take out Quan Chi and keep him from releasing Shinnok from the Netherrealm. In other words, he tries an Enemy Mine scenario with someone he knows is both untrustworthy and unlikely to help him, anyway. And what gives him the right to barter the souls of mortal men for Earth's safety? Yeah, he's the realm's protector god (which doesn't seem to mean jack, considering all of the times he's had to go behind the Elder Gods' backs in order to prevent Earth's destruction), but considering what we know of his past - especially his past with Shinnok, who tried something similar with Earth and got him kicked into Hell, as a result, how in the hell was he expecting to get away with this?
How, exactly, was Shao Khan able to Give the souls of the fallen Earth Realm warriors to Quan Chi in order to get help in invading Earth Realm?
Raiden surmises, at the end, that Armageddon can be prevented by letting Shao Kahn win, merge the realms, and be punished by the Elder Gods, as a result. Um... how, exactly? Sure, Shao Kahn will be gone, but he's left a Evil Power Vacuum that Quan Chi, and other known Outworld bigwigs have been chomping at the bit to fill, and that still doesn't take care of the issues with Shinnok and the events of MK4, or Onaga's resurrection or deception of Shujinko, or the corruption of Blaze and Daegon and the underlying problem of Armageddon - mainly that all warriors involved tapped into too much cosmic power and became too powerful to control. Hell, some of the characters' bios and endings (mainly Johnny Cage(?!) and Smoke) show that the warriors are already growing too powerful for the multiverse to handle. So, really, killing Shao Kahn in order to avoid Armageddon would be like trying to stop a flu pandemic from spreading more than it already has by washing your hands and getting a good night's rest.
One could interpret it as Raiden trying to stop the particular Armageddon scenario seen at the intro; Shao Kahn winning the power of Blaze and ending the realms. This doesn't stop Armageddon in and of itself, only Shao Kahn's victory. Also, at least in story mode, a rather large amount of the powerful warriors end up dying anyways; if it's treated as canon that could stave off Armageddon.