The story of the Brotherhood begins shortly after the end of the Second War, when the Alliance forces retook the Kingdom of Stormwind from the Orcish Horde. A major reconstruction project was launched by the Human nations of the Alliance to rebuild Stormwind, fueled primarily by those that had been driven from their homes by the war. When reconstruction was complete, the artisans, engineers and carpenters who had participated demanded payment for their contributions, and rightly so.
What happened next was something none of them expected: Stormwind's nobility denied them payment entirely. Various excuses were made, such as the rebuilding was considered a civil service, or the Kingdom simply did not have any funds to pay them. The craftsmen did not back down, so the Kingdom of Stormwind did the logical thing and exiled every single one of them from the city they worked so hard to build. Okay, so maybe it isn't logical at all, but that's precisely what happened. They were exiled and forced from the city.
Distraught, distressed, and cast out from their homes yet again, these people turned to a man by the name of Edwin VanCleef. VanCleef was not only a master engineer, but the head of the Stonemasons, a guild of artisans and craftsmen that had been contracted by the Stormwind Nobility themselves. No, they weren't paid for their time either. Unknowingly, these people made the wisest choice possible. Edwin VanCleef had a second, hidden life. He was once trained by Mathias Shaw, one of Stormwind's finest assassins.
Edwin VanCleef organized these men and women and they took on the name of the Defias Brotherhood. Justice was their goal, and they would get it their way. Red bandanas and tattoos of a cog on their palm would be the signs of their allegiance. Though the Defias began as simple craftsmen and artisans, any with the drive and ability could join their ranks. Outcasts of society were their greatest source of manpower. Orphans, halfbreeds, or simply those disillusioned with the world as it stood flocked to the Defias in droves.
It wasn't only the civilized races of Azeroth that flocked to the Defias, either. Their influence spread to the 'lesser' races of the region. The kobolds and gnolls of Elwynn Forest and Westfall worked for VanCleef, acting either as extra muscle or suppliers for their various projects.
Some of Stormwind's greatest minds were among those exiled, and the Defias wasted no time putting those minds to work. While the muscle robbed, raped and pillaged, the minds worked diligently behind the scenes, in their underground headquarters of the Deadmines. These engineers supplied the bandits and 'soldiers' with explosives, weaponry, and traps that would stop whole caravans in their tracks and leave them ripe for the plundering.
Their influence spread throughout the Kingdom of Stormwind. The Stormwind Guard did their best to keep the Defias under control in Elwynn, but they were couldn't (or wouldn't) allocate resources to Westfall or the other outlying areas. The locals to these areas were essentially left to fend for themselves against this army of bandits, which led to the creation of neighborhood militaries, such as the People's Milita of Westfall.
The local militias did little to slow the Defias for a long time, and rumors of the Defias building an 'unstoppable weapon' were spread. It took a few years of the Defias running largely unopposed, but eventually a group of brave, courageous adventurers finally discovered who was behind the Brotherhood, and retrieved his head. Not without some interesting discoveries, however.
First, the Deadmines wasn't simply the Defias hideout. The Deadmines was being used as a production center. For what? A massive battleship. Purpose? Unknown. Additionally, VanCleef's first mate is a Tauren. Strange, but not too unusual given the Brotherhood's tendency to attract the eccentric and outcast.
More unusual is that Defias activity never actually stops with the death of their supposed leader. Riots have broken out in the Stormwind Stockades, with the Defias at the helm. Some investigation uncovers their ringleader, and their accomplices. Bazil Thredd, VanCleef's Lieutenant, is promptly slain. Their accomplice is a man by the name of Lord Gregor Lescovar. A member of the Stormwind Nobility. Lord Lescovar and his hired blades are also swiftly killed.
Once this is done, Lady Katrana Prestor hears the news and applauds your efforts and informs you that the King will be unable to do the same. He's currently away on a diplomatic mission.
Enter: The Missing Diplomat. I'll not bore you with the details of the entire questline, that can be found on Wowwiki very easily, but I can sum it up for you. That diplomatic mission the King went on? As the quest name suggests, he went missing. He never made it to his destination. On the bright side, he isn't with the Defias either. They're most certainly involved... but they lost him. Yeah. Well done.
This mission was, apparently, to meet with Lady Jaina Proudmoore in Theramore. The Defias Brotherhood is definitely active off of the coast of Dustwallow Marsh, having suffered some major shipwrecks. It seems they were en route to an island not too far off shore. Jaina requests an investigation, and something much more serious than a simple band of thugs is discovered. The island is infested with Naga. Not only Naga, either. Dragons. Black Dragons.
If you haven't put two and two together yet, I'll nudge you in the right direction. Who do we know that is close to the King of Stormwind and is affiliated with the Black Dragonflight? Yes, that's right. Lady Katrana Prestor. Onyxia. It is very likely Katrana Prestor had her hands in this mess since the beginning, being a member of the House of Nobles herself, though not legitimately. Like Deathwing before her, Onyxia is working diligently to worm her way into the highest ranks of the surviving Human Kingdom, to bring it down from the top. It is extremely likely that it was her that exiled the Stonemasons from Stormwind.
Revealed in the Warcraft comic book, there's another party that has taken an interest in finding, and killing, the King of Stormwind. Magatha Grimtotem of the Grimtotem Tribe. This may be linked to the fact that Varian Wrynn was kicking ass and taking names in the arena against her prized fighters, but there are hints to the contrary. Remember our Tauren friend from the Deadmines, Mr. Smite? I think we can make a pretty safe guess here. Hint: He's probably a Grimtotem.
On a smaller but still noteworthy note, a note passed between the Bloodsail Buccaneers in Stranglethorn Vale suggests that they, too, are working with the Defias. A bit of a surprise, certainly, but it makes sense considering the Deadmines opens up to a river in Stranglethorn. There may be other parties involved in this conspiracy, too. We don't really know how deep this runs. It might be even bigger than we think. After all, I think there were some undead just outside of the Deadmines...
That pretty much brings us to the present in Warcraft. The story of the Defias and Varian Wrynn is currently in progress, and I'm sure we'll see many more revelations in Wrath of the Lich King. If you want more information on the Defias Plot, I strongly recommend doing the quests related to them and reading the World of Warcraft comic. If you don't have any Alliance characters, you should give it a shot anyway, at least up through the Deadmines. And of course, as always, Wowwiki is a good reference for anything you want more details on. I do my best to give you the full view here, but there's always little hooks and details that make experiencing the story yourself worthwhile.