Unknown to Nefarian, or Onyxia, there was another black dragon that took up Deathwing's banner -- or rather, took up his cause for her own evil gains -- Sintharia, mother of Onyxia and Nefarian, and Deathwing's prime consort. After Deathwing's madness overtook him and his body changed, he attempted to mate with his consorts. Being a creature largely composed of molten lava; this didn't really... go very well. In fact, Sintharia was the only consort of Deathwing's to have lived through the experience, and half of her face had been burned away in the process. Ouch. Sintharia had been presumed dead after a fight with the Kirin Tor, but it turns out she, much like Deathwing himself, merely went into hiding.
And what a hiding it was. Calling herself Lady Sinestra, she sought to complete what her mate could not hope to accomplish, and rule the world on her own. For Lady Sinestra had done the unthinkable -- somewhere near Grim Batol lay the shattered remains of the Demon Soul, and Sinestra found the shards and reforged them into a new Demon Soul, shielding it from all Azerothian magic so that it could not be destroyed again. With it, she could breed her own flight of superior dragons and keep them firmly under her control. She used the Demon Soul in combination with another artifact called Balacgos's Bane -- an object designed by the blue dragon Balacgos to absorb unharnessed latent magic and keep it out of the hands of people that would use it for ill purposes. But the artifact backfired, absorbing the dragon's magic and leaving him a lifeless husk.
The third element Sinestra used was a nether drake. Way back when the Dark Portal was opened for the second time, nether drakes attempted to swarm through to Azeroth, and promptly found themselves killed by the blue dragonflight. But the blues had missed one drake, Zzeraku, who was captured by Lady Sinestra and taken to Grim Batol for the purposes of feeding his essence to her warped young.
What else would a dragon need to make babies...oh that's right, eggs. Good thing there were all those leftover eggs in Outland from Deathwing's attempt to take it over. Players can check out Lady Sinestra, curiously devoid of any disfigurements, on Netherwing Ledge at the Dragonmaw Base Camp, paying Overlord Mor'ghor a visit. They have a nice little conversation about the state of Azeroth, Nefarian's failures, her master's work, and eggs. In exchange for the eggs, Lady Sinestra offers the backs of her drakes, to ride upon as needed. Sinestra takes off, leaving a bewildered Overlord to ponder what he's just been told -- that Deathwing is alive, and plotting something.
Only he wasn't, really. Lady Sinestra, ticked about the general state of her body because of Deathwing, her children's failures to accomplish anything worthwhile, and just all around angry at the world in general decided she'd much rather have the whole thing to herself. Herself, and her charming and well-mannered new babies.
These dragons, dubbed Twilight dragons by a draenei priestess named Iridi who had been sent to free Zzeraku from his imprisonment, were unlike any dragon flight seen previously. Much like the Chromatic dragons from Nefarian's experiments, the Twilight flight started out as regular, old-fashioned eggs from any of the five flights out there. Once the eggs were procured, they were fed the essence of other flights, and then imbued with the essence of the nether drakes. Sinestra had dozens upon dozens of these eggs, merely waiting for the magic infusion that would make them whole, hearty, and deadly. Her first two children failed, destroyed by Korialstrasz and Kalecgos, but the third lived and grew larger than his mother's fondest expectations in the depth of Grim Batol, carefully watched over by Sinestra as he grew.
However, with Korialztrasz, Kalegos, the previously mentioned draenei priestess and a slew of other people working against her, Sinestra would not succeed with her plans. Once again, the Demon Soul was destroyed -- this time not by Rhonin, but by his wife Vereesa. She used a staff that Iridi carried with her from Draenor, thinking that if nothing Azerothian could destroy the thing, perhaps something Draenic in origin would do. It did, the Demon Soul shattered, Sinestra went just as insane as her former mate and tried to put it together a third time, and Korialstraz hucked Balacgos's Bane at the twice-destroyed artifact, shattering it utterly. The Demon Soul was destroyed. Again. For good. We hope.
Sintharia's plans fell apart around her. No longer able to control her new child via the Demon Soul, it turned against her, destroying them both. Grim Batol collapsed inward upon itself, destroying the remainder of the Twilight eggs Sintharia had been experimenting on. Sintharia, along with her failed experiment of a child, were both destroyed and the world was safe once more.
Again, sort of.
Deep beneath Grim Batol, we're talking way, way down underground, Deepholm if you will, Deathwing clutched the eggs he'd managed to swipe from Sintharia's stash. He had the foundation, and through his clever use of Sintharia as an unwitting puppet, he had the methods necessary to bring the Twilight flight to full fruition. In Wrath of the Lich King, his methods were apparently successful, as the Obsidian Sanctum now plays host to Sartharion, three Twilight drakes, and a host of eggs and whelps. Once a shrine, now breeding ground, this is why it is necessary for players to kill Sartharion and the Twilight drakes.
The black dragonflight, despite all appearances is far from defeated, although it seems that the purpose of the flight itself has gone from being watchers over the mountains and deep caverns below the earth to... genetic engineering and trying to produce a supreme race of dragonkind. Whether or not they are successful with this mission is yet to be seen, although hints at the contents of the upcoming Ruby Sanctum raid instance indicate the efforts in destroying the Obsidian Sanctum weren't enough.
One thing however is utterly certain: we haven't seen the last of the Black Dragonflight by a long shot, nor have we seen the last of its leader, who will be returning to the scene later this year in Cataclysm.