The questline begins with the Archivum Data Disc, a quest item that drops off of one of the bosses before you enter Ulduar proper (Flame Leviathan, XT-002 Destroyer, Ignis). It instructs you to bring the disc to a "device capable of reading it."
This device turns out to be The Archivum, accessible only after you kill the Iron Council. The Archivum that looks quite similar to the room in which you help Brann Bronzebeared defeat the Tribunal of Ages in the Halls of Stone. In fact, Brann Bronzebeard is already there! And here's where things get interesting.
The insinuation from the likely unfinished quests is that the Titans still have a functional servant, Algalon, capable of beaming information back to the Titans. He's inside of Ulduar, locked in the Celestial Planetarium, and he seems to know that Yogg-Saron's breaking free.
Why does this concern us? Well, Yogg-Saron is enough of a threat that if the Titans were to discover that he was free, they'd likely spite the face to cut off the nose, where Azeroth is the face and Yoggy is the nose. Brann insists that you find a way to stop Algalon from getting info to the Titans and sends you to the Celestial Planetarium to figure out how.
When you arrive, you discover that the door to the Planetarium is sealed and can only be opened with the Sigils that four certain Watchers carry -- Thorim, Freya, Hodir, and Mimiron. But defeating them isn't the only hurdle here. Brann's quests state plainly that you defeat the Watchers on their respective hard-mode difficulties or you can't loot their sigils.
Hodir: Before he smashes his first Rare Cache of Hodir. This is a clear timed event.
Freya: With all of her Elders up (told you). This is a Sartharion-style event.
Mimiron: Before the self-destruct mechanism of his private quarters goes off. This is an unconfirmed timed event.
Thorim: Before he falls completely under the thrall of the creature impersonating Sif. The nature of this hard mode is unknown.
When all four Sigils are collected, the raid gains access to Algalon and can stop him from sending the fateful message to our former benefactors. A final quest after his defeat sends you to Dalaran to meet up with Brann and Rhonin to send out a new message to the Titans -- likely that everything is a-okay, nothing to see here, move along.
This questline has interesting ramifications, because it shows that for high-end progression guilds, Yogg-Saron won't necessarily be the final boss of Ulduar -- you won't need to defeat Algalon for Yogg-Saron to be accessible, and Algalon may actually be the hardest boss in Ulduar. This shows that Blizzard is following through on its promise to allow raiders who want a challenge to have their own progression path by performing all of the toughest challenges Ulduar has to offer. I'm sure this means that the rewards for doing so will be great, and that Cory Stockton wasn't kidding.
There's still a few things we don't know, though. Is the data-disc a single drop or a raid drop? Is the quest repeatable? Do you have to do the quest every time you want to kill Algalon, or does it open Algalon to you permanently? I'm sure we'll find out as more information about Ulduar comes to us through the PTR. For now I'm satisfied in knowing that hard-mode progression is the way of the future, and I, for one, welcome our see-through sparkly overlord.
On an (almost) entirely unrelated note, the PTR quests also reveal just how you forge Val'anyr, the Gavel of Ancient Kings, the new legendary mace coming with 3.1. You collect forty shattered pieces of Val'anyr, then combine them to form the Shattered Fragments of Val'anyr. But wait! You have to actually put the thing back together!
Don't trip -- just toss them into Yogg-Saron's brain. You heard it here first.
Many thanks again to StratFu for their great coverage of the hard-mode quests and for filling in the parts I missed.
Patch 3.1 brings us Ulduar, dual specs, significant changes to all the classes, and more! We've got you covered from top to bottom with our Guide to Patch 3.1.