This all came about when GoonSwarm, as they're known to do, pulled a recruitment scam on Haargoth Agamar, a Band of Brothers director who was in the guise of an alt. The way this scam typically plays out is that a non-Something Awful member is allowed to join the corp, sometimes for a fee, and move their assets to a station held by the Goons. (GoonSwarm was born on the Something Awful forums and being a part of that community is required to join their alliance.) Once the time is right, they boot the individual from the corp and keep those assets. Essentially, it's griefing. Only in this case, rather than the victim becoming irate... he wanted to stay. According to The Mittani, resident spymaster of GoonSwarm, the Band of Brothers director found he preferred the company of his "enemies" to that of his friends.
Agamar then revealed his main character to be a director in the Band of Brothers alliance. It would be false to say that The Mittani turned Agamar into a double agent, when in truth he turned of his own accord. He provided access to the Band of Brothers director forums as a show of goodwill. From there, the plans were made to dismantle (quite literally) GoonSwarm's main rival. Once assured a place within GoonSwarm, Agamar proceeded to disband the Band of Brothers alliance using his director level access. In addition to shutting down the alliance, he cleaned out his corporation's ISK reserves and stole their dreadnaught (capital ship) fleet, which became a gift to GoonSwarm.
This is where the details get somewhat hazy, as CCP Games hasn't released an official statement on the matter beyond the volunteer-reported news piece. Despite numerous allegations and rumors, there is no evidence that account hacking or account sharing took place, and CCP Games hasn't provided comment on the issue.

Both BoB and GoonSwarm had the opportunity earlier today to express their views on the current state of affairs on the player-run EVE Radio, hosted by "Funkybacon." The show set a new record for EVE Radio with over 1800 simultaneous listeners. It featured Dianabolic, who is well-known to many EVE players as the CEO of Reikoku, formerly a Band of Brothers corporation. Dianabolic laid out what he knows about how the alliance was disbanded, catching BoB by surprise. He also announced that the former BoB corporations will, as of tomorrow morning, have joined an existing alliance in the game. Dianabolic didn't state which alliance for obvious security concerns, and although there's speculation as to which alliance it will be, the answer will not be known until Friday.
The Mittani spoke for GoonSwarm on EVE Radio as well, which is fitting as he was integral to the theft of BoB's alliance. He laid out the entire scenario for the listeners, right up to where things have played out as of Thursday afternoon. Both Dianabolic and The Mittani engaged in a bit of discussion which was tense at points, but made for a great show. Due to its overwhelming popularity the BoB/GoonSwarm interviews and debate are being re-broadcast and will also be made available for download shortly.
One of GoonSwarm's stated motivations from their early days as an alliance was to punish what they viewed as the arrogance of Band of Brothers. If they've held true to that ideal, stealing the alliance out from under BoB effectively means GoonSwarm has accomplished what they set out to do years ago. To add insult to injury, The Mittani has stated he'll be publishing the archived BoB director forums he gained access to for everyone to read. In the meantime, GoonSwarm and many other enemies of Band of Brothers are absolutely storming BoB's home systems in Delve, and chaos reigns. The political lines in EVE Online have been completely redrawn, and we suspect that the ensuing drama is far from over.
Update: EVE Radio has made their interview recordings available for download.
- Dianabolic from Reikoku, formerly of Band of Brothers