Within the Mortal Kombat series, there have been several alliances and series of factions throughout the course of the story. The factions are the larger, more significant groups from whom several prominent characters are members of, while the alliances are made up of a coalition between two or more characters with common goals to be achieved by working together.
The Shirai Ryu are a clan of Japanese ninjas in the Mortal Kombat universe credited with bringing ninjutsu and other secret martial arts to Japan from China, being a splinter faction from the Lin Kuei.
In the original timeline, the Shirai Ryu were wiped out by the necromancer Quan Chi in conjunction with the Lin Kuei, with the clan's only survivor being the undead revenant, Hanzo Hasashi, better known as Scorpion. In the original timeline, Quan Chi wiped the Shirai Ryu out as a reward to the Lin Kuei when their cryomancer assassin Bi-Han, better known as Sub-Zero, killed Hanzo to obtain the map to the Amulet of Shinnok. Hanzo returned to life as the undead Scorpion, consumed with vengeance, and eventually, when he entered into service as the Elder Gods champion, his clan was revived as undead like himself, much to his fury.
In the new timeline, Quan Chi again killed the Shirai Ryu in conjunction as service to the Lin Kuei, only this time, he was hired by the son of the grandmaster, Sektor, who reneged on payment upon learning Quan Chi had revived Hanzo Hasashi as his new warrior, Scorpion. After Shao Kahn and Shinnok's failed invasions of Earthrealm, Scorpion was revived and set about rebuilding his clan with survivors of Shinnok's war, his prized student being Takeda Takahashi, son of the blind ronin and friend of Hanzo, Kenshi Takahashi. While the Shirai Ryu were wiped out a second time by one of Hanzo's own students, Forrest Fox, who was possessed by the anarchist Havik, Hanzo and Takeda would work together to restore the clan a second time, and years later, Hanzo would learn of both Quan Chi and Sektor's involvement in his clan and family's deaths, and finally make peace with the current Lin Kuei grandmaster, Kuai Liang. Hanzo would kill Quan Chi sometime later, avenging the Shirai Ryu and his lost wife and child.
The Lin Kuei are a clan of Chinese assassins, who detest being referred to as 'ninjas', and are among the deadliest kombatants within the Mortal Kombat Universe. Children from all over the world are abducted and indoctrinated with the clan's beliefs, with any attempt in leaving the clan marking the deserter for death.
In both timelines, the most prevalent Lin Kuei are the cryomancer brothers, Bi-Han, and Kuai Liang, who have both used the codename Sub-Zero as their assassin moniker. Bi-Han would meet his death at the hands of his arch-nemesis, Scorpion, and return to life as the malevolent revenant Noob Saibot. Other prominent Lin Kuei are Sektor, Cyrax, and Smoke, with Sektor and Cyrax being the most infamous examples of the Lin Kuei's Cyber Initiative and Smoke, who was Kuai's best friend, being one of the Lin Kuei's unwilling victims of the initiative, in the original timeline while it was Kuai would become a cyborg in the new. In both timelines, Kuai Liang seizes control of the Lin Kuei and attempts to restore the clan's lost honor, taking on the apprentice Frost, who shares his abilities.
The new timeline reveals that Sektor is the son of the previous Lin Kuei Grandmaster, from whom Sektor would take control of the clan by murdering his father, and begin a forcible conversion of all non cyberized clan members, even beginning a cloning program to create completely loyal cyborgs in what would be called a Cyber Lin Kuei, with Cyrax as his right hand man. Sometime after finally being freed from both Quan Chi's servitude, and the mind control of Havik, Kuai Liang would train with master Bo' Rai Cho before taking on the entirety of Sektor's cyborg clan. Kuai would free Cyrax from Sektor's control and kill the mad cyborg, taking his head as trophy. Cyrax then activated his self-destruct protocols, destroying himself and all remaining cyborgs, and left the restoration of the Lin Kuei in Kuai's hands.
Kuai revived the Lin Kuei in Articka, and upon examining Sektor's memories from his still-living head, learned of his role in the destruction of the Shirai Ryu. After sharing this information with the revived Hanzo Hasashi, hostilities between the clans finally ended.
In both timelines, Daegon is responsible for the deaths of his father Argus, and his mother, the sorceress Delia. In the original timeline, Daegon was manipulated by the fallen Elder God, Shinnok, who desired for Daegon to ultimately triumph in his father and mother's quest to obtain the god-like power of the fire elemental, Blaze. Thus, Daegon formed the Red Dragon clan, named after his dragon Caro, to help him, and prepare for the eventual awakening of his older brother, Taven. Daegon took Mavado and Hsu Hao as his lieutenants, ultimately assigning them to complete the destruction of the rival Black Dragon clan, who had been former members of the Red Dragon who left, unwilling to uphold the clan's strict codes. In the original timeline, the Red Dragon nearly succeeded in wiping out the Black Dragon, but ultimately, Daegon would fail to defeat Taven and win the power of Blaze.
In the new timeline, the alterations made by Raiden to prevent Armageddon have changed the Red Dragon significantly. The clan is no longer stationed in Earthrealm, but Outworld, and instead of a connection to Blaze, the Red Dragon possesses significant knowledge of the Outworld Dragon King, Onaga. Though still commanded by Daegon, their presence is stronger throughout Earthrealm and Outworld, serving as a mercenary army to the highest bidder. Daegon also has an intense hatred for the 'traitor', Kenshi Takahashi, who infiltrated the Red Dragon under Special Forces orders. In retaliation, Daegon had Kenshi's lover, Suchin, murdered, and nearly killed his son, Takeda Takahashi. Daegon's loyal warriors, Mavado, and Hsu Hao, would meet their ultimate deaths and the majority of Daegon's forces would be wiped out serving the Outworld general Reiko and the chaos cleric Havik.
The Black Dragon is a clan of assassins, thieves, and mercenaries for hire, formed from a splinter faction of the Red Dragon clan, by members who were tired of adhering to Red Dragon's strict codes.
In both timelines, Kano is the most prominent of his clan, having served Outworld by betraying his home realm, and has an intense rivalry with the Special Forces members Sonya Blade and Jackson Briggs. Kabal is also a former member of the clan, who attempted to go straight and nearly succeeded. The majority of the clan was killed by Jax after Kano freed them from prison, the few survivors being Kano and Jarek. After nearly being assassinated by the Red Dragon Mavado, Kabal was nursed by to health by the chaos cleric Havik, who rekindled his anarchist views and inspired Kabal to revive the Black Dragon as an anarchist faction, with his two new recruits, Kira and Kobra sharing similar ideals.
In the new timeline, the Black Dragon was never destroyed thanks to Kano infiltrating Special Forces to impede their investigations, allowing several members of the clan to survive, though Kabal would die during Shao Kahn's invasion and be revived as one of Quan Chi's undead revenant slaves. Kano would continue to ally himself with Outworld, all the while playing both sides of the realm's civil war for his own profit.
The Special Forces is an elite para-military unit in Earthrealm, the most prominent members being Sonya Blade and Jackson "Jax" Briggs.
In the original timeline, Sonya and Jax were successful in their endeavors to destroy Kano's Black Dragon clan, with Kano and Jarek being the only members left to find and kill. After Shao Kahn and Shinnok's invasions of Earthrealm, the Special Forces was reorganized into the Outer World Investigation Agency, which recruited new members like the Lin Kuei cyborg Cyrax, the telekinetic swordsman Kenshi Takahashi and the police officer Kurtis Stryker.
The new timeline sees the Special Forces rise in prominence by a significant margin, the entire unit having aided in Earthrealm's defense against Shinnok's invasion. After successfully sealing Shinnok into his own amulet, the Special Forces was assigned by Raiden to protect the relic, and over the course of twenty-five years, Sonya Blade climbed to the highest ranks while reorganizing S.F. into a much larger unit capable of protecting Earthrealm from more invasions. Sonya would work with Kenshi and her ex-husband Johnny Cage in training a new unit comprised of fighters not only from Special Forces, but the Shirai Ryu and White Lotus Society as well. Jackson Briggs, though long retired, would return to serve as a consultant for the group.
White Lotus Society
In both timelines, the White Lotus raises and trains Liu Kang and Kung Lao to be the champions Earthrealm needs to ensure its victory against Shang Tsung and his master, Shao Kahn. The current Kung Lao is a descendant of the Great Kung Lao, a member of the order who defeated Shang Tsung five hundred years previously. Though, in the original timeline, this role was assigned to the Order of Light, the White Lotus has retroactively been retconned into serving the same function. The White Lotus trained not only Liu Kang and Kung Lao, but Liu Kang's friend Kai as well.
In the new timeline, the order continues to honor Liu Kang after his death by establishing a temple in his homeland, where Shujinko is master, and the order trained the former archer thief Kung Jin, a cousin of Kung Lao and a descendant of the Great Kung Lao.
Brotherhood of Shadow
The The Brotherhood of Shadow is a cult of demons and undead based in the Netherrealm. They worship the fallen Elder God, Shinnok, and aspire to aid him in overthrowing the Elder Gods in revenge for his banishment from their ranks.
In both timelines, the brotherhood is led by the necromancer, Quan Chi, who also serves as Shinnok's closest acolyte. The Brotherhood hired the Lin Kuei and the Shirai Ryu to obtain a map that would lead to where Shinnok's sacred amulet, one of the major sources of the Elder God's power, was hidden, and it was ultimately Bi-Han of the Lin Kuei who got both the map and the amulet from the four elemental gods protecting it. Bi-Han would face Quan Chi's loyal followers, Jataaka, Kia, and Sareena, before fighting the necromancer himself and stealing back the amulet from Shinnok. Though Bi-Han did not know it was a fake at the time, the real amulet in Quan Chi's possession.
After Shao Kahn's failed invasion of Earthrealm, Shinnok and Quan Chi would launch a two-fold attack against both Earthrealm and Edenia, the Brotherhood aided by Shinnok's Army of Darkness, but the fallen elder god would be defeated and vanquished once again.
In the new timeline, the Brotherhood is still led by Quan Chi, who is much more loyal to Shinnok and actively working to recruit souls of powerful fallen warriors. Working with Outworld during their invasion of Earthrealm, Quan Chi obtained dominion over several of Earthrealm and Edenia's warriors souls, bolstering the Brotherhood's ranks. After Shao Kahn's destruction at the hands of the Elder Gods, Shinnok was finally freed from his imprisonment in the Netherrealm and staged an invasion on both Earthrealm and Outworld, seeking to corrupt Earthrealm's lifeforce, the Jinsei. Though Shinnok was defeated by Johnny Cage and sealed in his amulet, Quan Chi and the revenants continued to roam free.
It was ultimately D'Vorah, a Kytinn from Outworld who had become drawn to the power of Shinnok's Amulet, who succeeded in regaining the amulet for Quan Chi, who freed his master at the expense of his life, but Shinnok would still fail to corrupt Earthrealm's lifeforce and ultimately be beheaded by a corrupted Raiden, leaving the fallen elder god in a state worse than death.
Forces of Light
In the twilight of Armageddon, the characters on the side of good who sought to protect Blaze and allow Taven to win his father's challenge joined together to face the forces of evil for one final battle. Gathered by Johnny Cage, the Forces of Light were the last bastion against darkness in the final battle of Armageddon, though ultimately, they would fail to protect Blaze, resulting in Raiden's last ditch gambit to reset the timeline to avoid the destruction of all realms.
Forces of Darkness
In the final days of the original timeline, Quan Chi and Shinnok would recruit the vast majority of the forces of evil to their cause with the promise of ultimate power to be won from the fire elemental Blaze. The large army that was the Forces of Darkness was born of the evil characters desire for power, conquest, and vengeance against their arch-enemies. Shinnok hoped to use the army as a means of distracting the forces of good and allow Daegon to win Blaze's power, with Quan Chi conspiring to use Rain, Argus's lost son, to usurp his master's plans. Unfortunately for all of reality, it was Shao Kahn who claimed the unlimited power Blaze offered.
The Deadly Alliance
The Deadly Alliance was a temporary alliance between two powerful sorcerers. Their eventual goal was to conquer Earthrealm by using the Dragon King's undefeated army. Because the army was mummified, Quan Chi needed someone who could reanimate their bodies. That person happened to be the shape-shifter Shang Tsung, who also lived in Outworld. Quan Chi told him about his discovery and his plot and they came to an agreement. First, they needed to remove the two most important obstacles that stood in their way. Their first possible threat was Shao Kahn. Shang Tsung presented Quan Chi before him and after a token display of loyalty, the two attacked, slaying the emperor.
It was later revealed, however, that they had killed only a clone of Shao Kahn, as the real Kahn had fled the palace when he sensed treachery in his weakened state. When the emperor's clone lay dead on the floor, Kahn's general Kano stepped out of the shadows and offered his loyalty to the sorcerers. At the same time, Noob Saibot attacked and mortally wounded Prince Goro at a command of Quan Chi, during an important battle between the armies of Edenia and Outworld. Due to Goro's demise, the forces of Edenia were forced to retreat. The two sorcerers then traveled to Earthrealm, through the use of a hidden mystical portal, where they ambushed Liu Kang, Earthrealm's champion. Shang Tsung disguised himself as Kung Lao and ambushed him. Thanks to Quan Chi's intervention in that battle, the sorcerers were able to win and Shang Tsung snapped Liu Kang's neck then proceeded to take his soul.
The two also recruited the oni Moloch and Drahmin to their cause, and after Quan Chi opened a Soulnado to use the limitless souls to revive the Dragon King's Army and restore Shang Tsung's power, the oni threw Scorpion, who had been seeking his revenge on Quan Chi, into the Soulnado, seemingly killing him once and for all. Ultimately, despite Raiden's best efforts to recruit warriors capable of stopping the two, the Deadly Alliance overcame Raiden's fighters and faced the thunder god in a final battle that saw him defeated.
With no left in their way, Shang Tsung and Quan Chi turned on each other, with Quan Chi emerging victorious. Before he could revel in his triumph, the Dragon King Onaga revealed his return and attacked Quan Chi to obtain Shinnok's Amulet. Quan Chi attempted to fight Onaga off, with even Shang Tsung and Raiden joining him in a desperate alliance to defeat the greater threat, but all three failed and Raiden released his godly essence in a final desperate attack that killed himself, Shang Tsung, and wiped out Onaga's army, while Quan Chi managed to flee, but Onaga survived, claiming the amulet for himself, thus ending the Deadly Alliance.
Noob Saibot and Smoke formed an alliance when Noob discovered the inert body of Smoke. Reprogramming the cyborg to remain loyal to him, he reactivated his nanotechnology, and formed plans to create an army of cyber-demons, using Smoke as a template.
Prior to their union, Noob Saibot and Smoke had no known previous affiliations with each other, except for the fact that they were both Lin Kuei warriors in their lifetimes. Noob Saibot was the original Sub-Zero (and the older brother of Kuai Liang, the younger Sub-Zero), whereas Smoke was the close friend of the younger Sub-Zero. Following his death, the original Sub-Zero would eventually become the demonic wraith known as Noob Saibot, while Smoke would be captured by his own ninja clan and automated into a cyborg, programmed to seek and terminate his close friend (who had led the Lin Kuei).
Both warriors were present during the events of Shao Kahn's invasion, in which Noob Saibot (under the orders of his new master, Shinnok) was to spy on the events of Mortal Kombat and feign an allegiance to Shao Kahn - for the time being. Smoke had gained Sub-Zero's assistance in regaining his memories and learned that he still had a soul. His soul was able to override his programming and thus became an ally of Sub-Zero's once more. Whether Smoke was able to fight alongside Raiden's forces or not is unclear; what is known is that Smoke was eventually captured by Kahn's minions and locked away in the prisons of Kahn's fortress, apparently a war trophy for the emperor. Smoke was shut down and remained inactive for many years.
During the aftermath of Mortal Kombat: Deadly Alliance and the beginnings of Mortal Kombat: Deception, the leaderless Noob Saibot found Smoke's inactive body in a prison cell. Realizing that Smoke would be the perfect template for Noob's ambition to create an army of cyber demons and to rule the Netherrealm, Noob Saibot reprogrammed Smoke and reactivated him, thus allowing his body to reshape (due to his nanotechnological upgrades). He programmed Smoke to obey him and only him without question. The two then headed for Outworld, where Noob Saibot began his journey to ultimate power. The two would fight the current Sub-Zero, Kuai Liang, and nearly kill him, only for Kuai to be saved by Sareena.
Eventually, Smoke would be saved from Noob's corrupting influence and rejoin the forces of good, ending their alliance.
Ferra and Torr are speculated to be a unique species of 'symbiotes' from Outworld, though little is known of their true origins. It is thought they were originally citizens of Outworld that were experimented on by Shang Tsung's Flesh Pits but this is unconfirmed. They were eventually found in the Tarkatan Wastelands by the Osh-Tekk warrior, Kotal Kahn, who recruited them to his cause after saving the two from the Tarkatans. Since then, they have faithfully served their new emperor in return for his rescue.