Either you believe the Core that "the Swarm is its enemy" or not, but if the Swarm was such a menace Vaelyn and the people camping in the Core would be gone by now. Not to mention it would have extended its reach far from a "hole in the wall in the middle of Tier 3". It doesn't help that Shadow Lairs are "alternate reality" dungeons.

http://img821.imageshack.us/img821/8272/hemustbedestroyed.png

(with power of friendship)

Don't be surprised if we end up fighting the Alpha Squadron when the Core opens. Once we defeat them we realize it's all a plot and the Skylark gets ambushed.

I was always under the impression that Cradle was built as a prison. The impenetrable shell was built around the core to protect whatever is inside*, and when the swarm came to attack it the gremlins built the different floors around it to keep it trapped. They constantly shift and rotate to ensure that the Swarm never finds its way out.

*I also believe that Sanctuary is inside the core itself. If you'll remember the core opened to save Alpha Squad in a situation very similar to the Unknown Passage, and the inside of the core is described as a bright white light. You escape the Unknown Passage into a similar bright white room which seems to be sentient and seems to save you on purpose. The only flaw in this theory is that it offers no explanation of what happened to the Alpha Squad; you are dropped at the core terminal when you leave, but perhaps the Alpha Squad went further into the core or was ejected into an unexplored area of the Clockworks.

SL is not alternate realities. They are real just like any Clockwork levels. Except that the programming logic was corrupted and so it became imbalanced (that applies to the rewards also). Remember Cradle reconfigure itself? There should be a control system somewhere, right? Somehow the Swarm, originally benign, got out and turned against their creator (the Architect). They infected part of that control system to create dangerous levels that they use as both defense system and as traps for their preys.

SL connects to Sanctuary because it is what that stopped the Swarm's infection. The Unknown Passage is where the Cradle control system fights off the Swarm's infection. That's why when you compare Unknown Passage to SL levels, the SL levels are clearly more stable and don't collapse like Unknown Passage.

The Cradle control system lies inside the Core. Therefore the Sanctuary is inside the Core and probably serves like a Tier 1 weapon locker for the Core's guardian. When you exit Sanctuary, you are returned back to the entrance of the Core so you can fight off the Swarms.

I think the word "Swarm" is a big give away of what they are. They are nano machine colonies that either went out of control (hinting at a new enemy => DLC) or they gained a Swarm mind of its own and rebelled against the Architect.

Because Vanaduke is trapped as a kind of program inside the Cradle's control system. It gets reconstructed every time FSC is generated inside Clockworks. The Duke, Almirian and the countries they were at war with, were both long gone according to lore. i.e. they killed off each other, leading to an opportunity for Gremlin's colonization.

The indicator anomaly was due to Swarm interference. As you can see when you reach Unknown Passage, the interference was strongest because the Swarm was at war directly with the Cradle's control system. Of course there are Swarm Seeds inside SL, because that's what infected part of the Cradle's control system in the first place. And they couldn't be eradicated by brute force, as brute force only suppress them. You need a strong energy source (like the Core) to cleanse them.

As for the messages left behind in Sanctuary, it really depends on who left them there. My theory is that they are holographic recordings left behind by the Cradle's control system. That's why the messages talked about the Architect and the Swarm in third person, and it blames the Architect as the cause of the Swarm (which he is because he engineered the Swarm).

The Gremlins were colonists, as the lore tells us they aren't residents of the Cradle. So it's safe to assume the Architect together with the Gremlins were sent from their home world to Cradle for colonization. Then one day, the Architect got lazy and thought "you know what, let's create these nano machines do the works of us while we go pet those cute Snipes!" But little does he realize a collective mind emerges from the nano machines and it turns against him.

The Swarm got out, infected everything (including the Architect, leading to his madness), the Architect with his last sanity put himself into stasis, left warnings behind and let the Cradle's control system took over. The Skylark caught the signal ("DO NOT APPROACH, I REPEAT, DO NOT APPROACH"), got attacked by Swarm in orbit, crashlanded on Cradle and leads to the beginning of Spiral Knights.

The dialect ship in Ghost in the Machine probably caught the same signal also but them being a smaller ship, was less fortunate than the Skylark.

So you're saying the core is like a living battery and cradle was built so space pirates don't drain it.
The swarm are gremlin nanomachines that became self aware skynet-sytle and want to use our ship to escape.

I think you are reaching too far, I mean, I did too when I made my theory pro-Core months (a year?) ago, but I didn't think on the whole "illusion" possibility which other people suggested, and again, about the two Vanadukes: how they can be two of them. And I don't mean "reconstruct him". In Arcade, there is in the same floor to the "Shadow Lair passages" a way to go to fight Vanaduke if you go to his gate. Vanaduke is there, down there, if you got far reaching binoculars you may see him down there waiting in his throne straight on in a path far away. And then, you can go another way going through unknown, mysterious undocummented ways in the Cradle rotation to ANOTHER Vanaduke. Vanaduke being a UNIQUE being made due to Vog's curse. There can't be TWO Vanadukes at the same time, same as the Roarmulus Project - you could do another factory, but again wouldn't make sense due to its "location ready to take on Haven when ready".

The messages are confirmed to be recorded by the entity which resides in the Core - "it was made to protect me". Now, what it says may be true or not... and I totally think it is double-crossing us now. Also, if it was made to protect the entity, and you say that the Architect created the Swarm, the Core was made then from night to day once the Swarm "got mad"? I think not. According to the entity, the Swarm and the entity existed since ancient times and the Architect made the Core structure to not let the Swarm get in. Which means... the ancient tribes fought there the Swarm along with the Gremlin colonists while the Architect made the Core, and shut there the entity instead of the Swarm which would actually pay off...? And Cradle isn't infected 100% with Swarm already because...?

The Core is a sealed evil in a can, and it made us crash and is fooling around with us to make us his/her puppets. In fact, I wouldn't be surprised if the Strangers knew more than we know. The Core may not have an evil look but it is really powerful, and once we get "rid" of the Gremlins it will open up, welcome us, go with us back to our planet... and then all hell will break loose. And we will be its obedient army and expand its reach with our technology.

Also, Ghosts in the Machine lore is your typical Matrix/Ghost in the Shell (omgname) lore and it doesn't have anything to do with the Swarm.

Which again, would mean there would be two Vanadukes at the same time in two different places.

Being inside Core = Architect in stasis. Why? Because he was infected and became delusional. But he still hold the key to unlock the Core because he is the Architect after all.

It's very simple actually. Because those messages were meant to be ambiguous. So we think there is "someone" inside the Core for the Clockworks to protect. OK, but who is this someone that is worth so much effort to protect? The Architect, but only if he holds the key to something even more valuable.

If this is a simple mining colony, it's not worth the effort to put a self reconfigurating fortress on top of it. That's why it has to do with energy, and probably an infinite source.

What I believe throw people off here is that the messages were ambiguous enough to hide the most important question: why the Clockworks was here in the first place. It's artificial and it's meant to protect something valuable enough to worth the effort. So the most likely logical explanation is that the Core has a (close to) infinite energy source that the Gremlins can harvest for eons.

Don't get fooled by those messages in SL. They are ambiguous enough to fit into many interpretation. Focus on the only question that matters: what exactly is the Clockworks designed to protect? If we know what it is to protect, then we know who will be interested in it.

I believe the Swarm is a very minor thing. To me it fits into the description of an experiment with good intention but goes horribly wrong.

Aumir, how can we kill vanaduke, twins, snarbolax so many times??

I think you're being too nitty gritty about it. There will always be such plot fallacies in an MMO game. Either you go down normally. Or if you go down a different way, it's been infected by the swarm.