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The Hidden Swarm are a brood of the Hive previously under the command of the Hive god Crota and his disciples, led by the Swarm Princes under their commander Sardon, Fist of Crota. Since Crota's demise and the genocide of his spawn, the Swarm became the de facto Hive power on the Moon; succeeded by Crota's own daughters.
The Hidden Swarm are the first Hive encountered in The Dark Within. On the Moon, they're the outermost defensive line, warding off anyone attempting to enter the Hellmouth. They are identified by their red-orange coloring and the large nails driven through their arms and bodies. This sect of Hive is encountered once more on Luna in Shadowkeep; their general look remains the same compared to Savathûn's Hive but they now seem to have some form of spiked growth all over their bodies.
Arrival in the Solar System
When Crota, Son of Oryx and his spawn arrived at the Solar System and took over the Moon, the Hidden Swarm served as the beachhead force for Crota's staged invasion of Earth and also tasked with protecting their newly erected lunar strongholds, the most infamous of which being the Hellmouth. As they silently built their strength over the centuries, a Titan named Rezyl Azzir happened to intrude upon the Hellmouth and met with the Hive Wizard Xyor, the Blessed and her consort Knight. Though Rezyl survived his encounter, it would ultimately be Xyor's plan to curse the Titan with her dark whispers into becoming the infamous Dredgen Yor.
During the early City Age, the Hidden Swarm launched their Seeder Ships throughout Earth and engaged the Light-bearing Guardians at the Rusted Lands in the Eastern Flooded Zone; only one surviving Hunter warned the City of the Hive threat. Against overwhelming odds, the Guardians barely succeeded in repelling their forces at the Battle of Burning Lake, only to fail at their counteroffensive at the Great Disaster on the Moon.
Unopposed after their victory at Luna, the Hidden Swarm continued to seed their brood in secret beneath Old Russia for years, until Fallen from the House of Devils stirred them up at Skywatch much to the discovery of a newly-Risen Guardian.
With word reaching the Speaker about the resurgence of Hive activity on Earth, a Vanguard scout was sent to investigate the fortified Hellmouth for answers; His trail lead him to the entrance of the Temple of Crota only to be killed by the Hive. His Ghost was held captive by Vurok, Eir Spawn who probed it of information for study; the Ghost would likewise gain glimpses of the Seeder Ships prepared for invasion before expiring. Coming to the Moon for the first time, the Guardian would trace the deceased scout's location, where they faced Vurok and recovered the dead Ghost. From probing its memories, they soon got confirmation that the Hive were indeed preparing a second attack on Earth.
Upon further inspection of the dead Ghost's memories, the Guardian's Ghost uncovered the existence of The World's Grave, a vast archive chronicling everything that the Hive had known of Earth. Delving into the depths of the Hellmouth in search for insight into the enemy, the pair killed Kranox, the Graven and loot his key to the archive itself. Upon further investigation, the two would fully realize the scope of the Hive's plans of seeding the Earth for centuries in preparation of Crota's second coming, which they would warn the City of the impending danger.
By then, the Hive had began a ritual draining the Light of the Traveler using a corrupted shard of it, causing the Speaker to issue an emergency broadcast to all Guardians to stop it. The Guardian would answer the call, battling deep through the Hellmouth and into the Chamber of Night where they were successful in stopping the Siphon Witches of their ritual.
At the same time, the Wizard Mormu, Xol Spawn had raised an unstoppable abomination called Phogoth, the Untamed, a massive Crota-spawn Ogre bred for destruction since the Great Disaster. Because of its savage nature, Phogoth was kept alive through foul rituals of rebirth and chained up in the Summoning Pits. However, their activity quickly alerted the Vanguard who called a strike team to action, killing Mormu and destroying her creation before the Hive could unleash it upon Earth.
The Guardians would later come to the Hellmouth seeking Thorn, the most infamous of the Weapons of Sorrow once wielded by Dredgen Yor after he was corrupted by Xyor, the Unwed into becoming a Guardian killer. After recovering the cursed Hand cannon in the Summoning Pits and cleansing it with Light, the Guardians killed the Wizard responsible for Thorn's creation as a final step to claiming the weapon as their own.
The Hive's activity were pacified thanks to the actions of the Guardians, but the threat of Crota's return remained; one which would be addressed by the former-Lightbearer Eris Morn. Having sworn vengeance on the Hive and their master Crota for the losses of her Light, Ghost, and fireteam, Eris took tactical control over the Guardian operations as they work to dismantle the leadership behind the Hidden Swarm, including the legendary Swarm Princes (whom forged Crota's infamous Sword) and their commander Sardon, Fist of Crota (whom lead the Hive spawn on Earth). Eventually, Crota fell to the Guardians, though word of his death would reach his father: Oryx, the Taken King.
Following a year after the Taken War and the death of their God-King, the Hidden Swarm on Earth still appear to be organized but hunkered down in their nests, and have recently gone into conflict with the SIVA-augmented Fallen Devil Splicers in the Plaguelands. Soon enough, the ambitions of the Splicers, led by Kovik, Splicer Priest, extend to experiment on not only themselves but the Hive as well, whether to control them as a slave army or to weaponize their mysterious biology. Furious, the Hive begin an all-out war with the Splicers. Through the efforts of the Guardians (not out of pity), the Fallen's efforts to control or weaponize the Hive were thwarted and Kovik was killed.
Years after Crota and Oryx's deaths, the Hive on Luna would remain relatively quiet. As the attention of the Guardians became preoccupied with the chaos of the Red War, the conflicts on Mercury, Mars, and in the Reef, the Hive on Luna would be overlooked. As a result of numerous deaths, the various broods on the Moon consolidated into the Hidden Swarm, becoming the "de facto" Hive power on the moon. However, the toll of the Taken War had left the Hidden Swarm bereft of warriors of a caliber befitting royalty that could lead the Hive on the Moon. Crota's brood rallied around the strongest of his children, including his four daughters Besurith, Kinox, Hashladûn, and Voshyr. While the Swarm attempt to reaffirm their belief in the sword logic, the daughters of Crota held faith in the belief of Oryx's second coming and schemed to recapture the greatness of their lineage.
Hashladûn and her coven of sisters saw an opportunity in the Lunar Pyramid's power and its connection to the Darkness as the means to conjure back their grandfather, the fallen Oryx, in the shape of a Nightmare and exact their vengeance against the Guardians for ravaging their lineage. However the Hidden Swarm was soon marred by corruption and conspiracy from within, as Hive distrusting of the Daughters' leadership enact a conspiracy to usurp them using forbidden sorcery in defiance of Oryx's Sword-Logic. Their conspiracy failed as it was all a ploy orchestrated by Savathûn, the Witch-Queen to help further her greater schemes, in exchange of aiding her grand-nieces in giving them necessary tools to challenge the Risen. 
Over the course of years, the Hidden Swarm constructed a massive crimson fortress, the Scarlet Keep, before the Pyramid that would act as an amplifier for their magics and could immunize themselves of the Pyramid's influences. They would then bid their time for the opportunity of its eventual awakening, with the one behind Oryx's killers acting as their catalyst while manipulated by the Witch Queen of her curiosity. 
Eventually, the discovery of the Pyramid by Eris Morn provided such an opportunity, creating phantasmal Nightmares based on the Guardians' traumas that the Swarm could exploit in the battle to come. Within hours, Seismic activity erupted across the landscape above the Pyramid, cracking the surface of the Moon and causing the Hive to frenzy; to which the Vanguard would deploy a massive siege operation upon the gates of the Keep and secure ground at Sorrow's Harbor.
The Guardian would soon enter the Scarlet Keep to investigate but would soon discover the Pyramid and encounter the Nightmares for the first time, nearly getting overwhelmed as the Nightmares took the form of Crota, Dominus Ghaul and Fikrul, the Fanatic. Fortunately, Eris Morn would rescue the Guardian and soon lead the charge against the Hidden Swarm. Gaining the Vanguard's support, Eris Morn guided the Guardians into dismantling the Hidden Swarm's power base while seeking a way to enter the Pyramid.
The Hive began to summon Nightmares near the Scarlet Keep starting with the Nightmare of Gothrax, Swarm Protector. Using a forbidden piece of arcane knowledge, the Cryptoglyph, Hashladûn and her sisters experimented on the phantasmal Nightmares created by the Pyramid only for their efforts to be fruitless as they could not raise their father nor grandfather; their essences having truly dissipated and that the Nightmares were not alive. Kinox instead saw another opportunity to use the Nightmare essence in a manner previously provided by the Witch Queen.
Unfortuately, the Guardians would soon confront Hashladûn herself within the Keep, slaying the eldest of Crota's daughters at the peak of the Tower of Woe. Further on, the Guardians braved the darkness of the Hive's most forbidden sanctum, the Catacombs, to acquire the Cryptoglyph so Eris could create armor to combat the Nightmares, slaying Besurith, Daughter of Crota in the process. Such actions were critical blows to the Hidden Swarm but they would remain a threat the Guardians continue to fight against as well as containing the Nightmares.
Return of Zulmak
Currently, the last of Crota's daughters, Voshyr and Kinox, remain in hiding to continue their heretical work; going against the Sword-Logic for the sake of survival. Having learned from Hashladûn's attempt to preserve their family's past glory, Kinox took the opportunity to made use of a weapon they gained following the failed conspiracy within the Pit beneath the Scarlet Keep: a fallen Knight reanimated into a hybrid between the Hive and the Nightmares yet bound to their whims.  Using demented rituals that involved sacrificing Nightmares into an crystal that empowers Zulmak, Instrument of Torment, the surviving daughters of Crota could use their puppet champion to rally the leaderless Hidden Swarm against the Guardians. However, as their rituals caused seismic disturbances, the Guardians were alerted to their activities.
Delving deep beneath the Keep, the Guardians explored the Pit of Heresy and encountered powerful Hive, Disciples of the Broken Blade. After slaying each disciple and solving intricate puzzles, the Guardians managed to reach Zulmak's lair, the Cradle of Damnation. There, the Guardians faced off with the Daughters' puppet but despite his strength and the power gained from the sacrificed Nightmares, the Guardians used his own Swords and magic against him, bringing the monster down.  However, due to the Daughters' desire for revenge, they would continuously revive Zulmak after every slaying and attempt the same ritual, forcing Guardians to contend with the abominable Knight in the Pit for an seemingly unending period of time. 
The Scarlet Court's Fall
A full year after Hashladûn's demise left the lunar Hive leaderless, the broken Swarm began calling out to Xivu Arath, God of War in wake of the Black Fleet's arrival and prayed to be recommitted into the fold. Acting as the God of War's envoy, the High Celebrant of Xivu Arath came to Luna to wrestle the Swarm free of the exiled Witch Queen's plans and instead reform Luna in Xivu Arath's image: A world where all tithes were tribute to her. Almost a week after the events on Europa, the warlock Osiris had also tracked the most potent of the Cryptoliths' signals across the Solar System to the Moon. Beneath the shadow of the Lunar Pyramid, Osiris found the entirety of the Scarlet Court, including the remaining kin of Crota, communing with a visage of Xivu Arath alongside her High Celebrant.
In an audacious and "suicidal" move as described by Sagira, Osiris descended upon the gathering as the mighty Phoenix he was and began to slaughter the court. Voshyr and her two daughters Yishra and Ayriax were the first to perish before they could even finish their incantation - incinerated by Osiris' Daybreak. Kinox was also vanquished attempting to flee into the crevices with her son Ulg'Urin and his cohort of Knights having died in defense of a massive Nova Bomb. The remaining lesser nobles were killed in the slaughter, which filled the Hive god of war with power from the Warlock's violence. Osiris was then stripped of his supers when the visage and will of Xivu arath emanating from the large Cryptolith taunted him. Osiris was pinned and around him were cleaved Runes in the stone by the High Celebrant. In a stunning and tragic act, Sagira broke through the oppressive force Xivu projected that was slowly killing Osiris and sacrificed herself - destroying the Cryptolith and projection, saving Osiris but leaving him Ghostless. The light in the place of Sagira's sacrifice remained for days.
With the demise of the Scarlet Court came the end of the Taken King's lineage with no surviving heirs of Crota left; the remaining Hive had pledge themselves to Xivu Arath as their only master. One Knight, Kelgorath, Risen from Bones would renounce his ties to Savathûn and leave the Swarm to become a powerful Wrathborn in service of the Hive god of war. According to him, Xivu Arath had rightfully avenged the deaths of Crota's kin by taking away Osiris' Light and Ghost. 
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