The 'cargo' Deathwing moved from Azeroth to Draenor was eggs. Dragon eggs that Deathwing had been stowing away for an opportunity such as the one just presented to him. Why settle for one world after all, when you can have two? Deathwing moved the eggs to Draenor, leaving some of his drakes to help the orcs as agreed upon, and taking the others to Blade's Edge. He took something else with him as well -- the Skull of Gul'dan, from Ner'zhul himself. After all, Deathwing reasoned with Ner'zhul, it wasn't as if he had a use for the thing anymore, since he had all the artifacts he needed from Azeroth. Ner'zhul agreed, reluctantly handing over the Skull.
But Draenor wasn't uninhabited by far -- Alliance forces had traveled through the portal, and stormed through Blade's Edge, allying themselves with creatures known as the Gronn. Led by Gruul, the Gronn were a little annoyed at the sudden intrusion by the black dragonflight, and preferred to have the nuisances eradicated for good. The eggs that Deathwing had so carefully transported were systematically destroyed. Well, almost. There were eggs remaining in other areas, but Deathwing, sensing the world about to be torn apart due to Ner'zhul's portals, escaped back to Azeroth, abandoning what was left of his flight and the eggs in favor of saving himself.
Back on Azeroth, Deathwing struck again -- this time at Dalaran, where he was soon 'defeated' and fell into the sea. The council of Dalaran assumed he'd perished there, to their folly. At the same time, a new noble arrived at Lordaeron's gates, making an instant good impression with all of the leaders of the newly formed Alliance. His name was Lord Daval Prestor, and his origins were unknown, but nobody really thought to ask. After all, he was terribly clever, well spoken and full of ideas to improve and solidify the shaky Alliance that had formed during the Second War. Popular not only with King Terenas, he'd also managed to impress Lord Admiral Daelin Proudmoore of Kul Tiras, Thoras Trollbane of Stromgarde, and surprisingly, Genn Greymane of Gilneas as well. The nobles had been bickering over who would take over the nation of Alterac, and Lord Prestor provided a tidy solution to the problem.
This, of course, was also a big fat lie. Lord Prestor was none other than Deathwing in human guise. He used his magic to bewitch the Alliance leaders, even going so far as to convince King Terenas that Lord Prestor made a more than suitable match for his young daughter, Calia Menethil. Deathwing's plan was to insinuate himself into the Alliance so that he could destroy it from within and wipe out the human race in the process, leaving him with less resistance as he tried to take over the world.
In the meantime, other events were going on -- the red dragonflight's leader, Alexstrasza, had been captured by the Dragonmaw orcs, imprisoned within Grim Batol and forced to produce endless amounts of eggs for the clan so that they could slowly rebuild their numbers and defeat the alliance with the red dragons firmly under their control. Rhonin, a mage from Dalaran, was sent by the Kirin Tor to observe the orcs and dragons so that a plan could be formulated to stop them. Deathwing 'saved' Rhonin, telling the mage that he wanted Alexstrasza freed in order to try and atone for his mistakes in the past.
Rhonin was also being manipulated by another -- the red dragon Korialstrasz, consort to the Dragonqueen herself, had disguised himself as a member of the Kirin Tor's council and sought to use Rhonin to free his beloved queen. What Rhonin didn't know however, was that the reason Alexstrasza couldn't just up and destroy the orcs imprisoning her was because an orc warlock named Nekros Skullcrusher had the Demon Soul. That's right -- wherever Malfurion hid it, he didn't hide it well enough. Nekros was given the Demon Soul by his chieftain, Zuluhed the Whacked, a shaman who didn't have much luck using the thing himself. Nekros had no clue exactly how vast the power of the little artifact actually was, but he was able to use it enough to kidnap Alexstrasza and Tyranastrasz, one of her elder consorts, as well some of her eggs.
Rhonin agreed to 'help' Deathwing, having very little choice in the matter and entirely too uneasy about the whole thing, for good reason -- Deathwing didn't want Alexstrasza freed, he wanted her eggs to use for his own purposes. After all, all the eggs he'd so carefully stowed away on Draenor were surely destroyed by this point. His purpose in egg collecting was simple -- to genetically engineer a new dragonflight. One that would be raised by Deathwing, a superior new breed of dragonflight that would carry his overwhelming hatred and distrust of the mortal races and lead the world into a land of chaos and destruction. Coincidentally, this was also the sort of thing the Old Gods were really keen on.
The plan failed -- Rhonin discovered the weakness of the Demon Soul. See, it'd been imbued with the essence of all dragons except for Deathwing himself, making him the only being capable of damaging or breaking the thing. Rhonin managed to get his hands on a piece of Deathwing, a portion of an amulet Deathwing had given him so that the two could speak. Using the gem in the center of the amulet, Rhonin shattered the Demon Soul, freeing the essences of all the flights that had been captured in it in the process. Needless to say, Alexstrasza wasn't particularly happy about being locked up and made to watch her children be raised as bloodthirsty savages. Malygos, who'd shown up to help out, wasn't exactly happy about his flight being nearly wiped from the face of the planet ten thousand years earlier, either. Ysera wasn't particularly pleased, and neither was Nozdormu -- and after having their full powers abruptly returned to them, the four Aspects quickly dog-piled on Deathwing with the intent of destroying him.
Deathwing, however, escaped. Barely. Coincidentally, Lord Prestor up and disappeared, and the Alliance went right back to their bickering over Alterac. Greymane withdrew from the Alliance; Trollbane quickly following suit, and the tentative Alliance of the Second War crumbled. So perhaps Deathwing accomplished something after all, even if it wasn't quite on the scale he'd hoped for.
Little was heard of Deathwing after that, although black dragons continued to terrorize the public at large. Two in particular were much more devious and cunning than most -- the favored children of Deathwing, Nefarian and Onyxia. When their father had traveled through the Dark Portal, he left them behind with a task to complete. While Deathwing had allied with the orcs of Draenor, Gorefiend and Ner'zhul's kind, there were orcs left in Blackrock spire led by Rend Blackhand. The Blackrock Clan had outright refused to join Gorefiend's Horde, choosing instead to forge their own Horde, and take over Azeroth on their own. Deathwing really didn't need the competition, so he asked his son Nefarian to infiltrate Blackrock Spire, taking control of the orcs within and making them little more than servants of the Black Flight.
The Black Dragonflight is not only intent on global supremacy, but racial supremacy as well. Deathwing was not content with any of the difference races of dragons out there for his disposal, he wanted something new, pure, raised by his own methods and utterly devoted to him in all things. His children eagerly followed suit with his purposes -- Onyxia holed herself up in the Wyrmbog and began producing eggs, attempting to single-handedly repopulate the black flight. However, she had another purpose in mind that she hoped would impress her father – where he had failed in his political machinations as Lord Prestor, she would succeed. Taking the name Katrana Prestor, Onxyia infiltrated the Council of Nobles in Stormwind and quietly sought to corrupt the kingdom of Stormwind from within, distracting them from her brother's activities in Blackrock Spire and keeping them firmly under control.
This plan was successful for quite some time largely due to Onyxia's successful capture of Varian Wrynn, the current King of Stormwind, his 'destruction' at her hands and subsequent 'reprogramming' making him a useful tool for her cause. Unfortunately, this backfired on her in a big way -- she sought to control King Varian by magically separating him into two distinct beings -- Varian Wrynn, the side of him that was weak-willed and easily controlled, and the other half of him that was dubbed Lo'gosh by the orcs that captured him. Lo'gosh was Varian's stronger side -- the side of him that would not bend to Onyxia's machinations. Lo'gosh managed to escape Onyxia's clutches and fight his way back to Stormwind in a series of adventures that were covered in the Warcraft comic series. Once Lo'gosh returned, he and his other, meeker half went after Onyxia and killed her.
This left Nefarian to his own devices, but Nefarian had plans to impress his father as well. Not only had he taken control of the Blackrock orcs, he decided to go one step further and engineer a new dragonflight for his father -- one that would be utterly under Nefarian's control. Taking eggs that were doubtless provided by his sister, Nefarian altered them using the essence of all of the different dragonflights. These new, horrific creations were what came to be known as the Chromatic dragonflight -- dragons with the properties of all five flights in one scaly and unpleasant package. Bred and raised in captivity, these dragons are highly intelligent, but know only servitude, and none have the power to break Nefarian's hold over them.
The Chromatic dragons were small in number, and located solely in Blackrock Mountain. After Onyxia's defeat, adventurers turned their sights on Blackrock Spire, and while Nefarian put up quite a fight, he was summarily defeated, his experiments dying with him.