This thread is about the backstory/lore of the game. All of my speculations are based off the most solid evidence given to us directly by the game, and then branch off logically. I am attempting to get the "for certain" story, not something that "could be right but I just wanna throw out a cool idea". This will be updated as more infor and such comes out, along with more solid theories and stuff.
All of this is saved on my computer with every update, for backup and my offline personal reference.

Think I figured it out, so...The below has possible spoilers of ingame stuff. Also be prepared.

Alright, lets start with Alpha Squad. Sent to Clockworks, never returned. All that's left are data entries left after each boss area or w/e. Now in the last mission( well playable one really) The King of Ashes, upon reaching the core, it is different than that of the arcade version. No one is there, that creepy music plays, and all thats there is now a new artifact left behind by none other than Alpha Squad.

What's strange is what is written:
"A Recording from Parma, Alpha Squad Recon:
We are at the end of the line. Pursued by some kind of terrible darkness we are forced into the unknown.
As we neared the Core- I don't know how to describe this really... the shadows came alive and began to attack us. Rulen became enveloped in it and by the time Grantz freed him his body was badly burned. He said it felt like both fire and ice.
And then we could go no further. As I record this, the darkness is nearly upon us, comsuming the world we see, the light.
But then the Core, it began to open, filling the place with such a light, such and intense, blinding light. Euclid has made the call; faced with the darkness, we'll enter the core, enter the light.
This will likely be my final recording."

Now we know 2 things based on everything so far, if you've looked into the lore on your own time as well.

1. Alpha squad had, for certain, traveled into the core before disappearing.
2. The core is said to give off a strange light. It also Is supposed to radiate Energy, which knights use to power stuff and stuff (lol great vocab there)

Now the third thing is what sparked my interest again. They say they were being attacked by a darkness, or shadows. They also say that it greatly hurt them when it "enveloped" one of their teammates.

I think its the Swarm (no durr). first of all, well, its darkness stuff. Basically manifestations of cradle's inhabitants in their most powerful forms.
What also ties into the mystery of the Swarm is the Echo stones and Sanctuary.

Sanctuary: My thoughts:
Ok nothing seems out of the ordinary of the place in itself to have a ton of lore. I think it's merely either A) a safehaven made by Tinkinzar, the Core's essence, or Alpha Squad's manifestation of thoughts of a safe place (which makes the alchemy station there exist).

It is NOT inside the core, as traveling deeper takes you to the outside of it. It seems to be merely a wall between the Swarm infected areas, and the core itself.

Back to the Echo stones, they reference The Architect (King Tinkinzar) and the Swarm. It says, based off of the UFSC stone:

"As I dreamed, it consumed.

It devoured the knowledge of time... Memories of the dead... The hearts of kings and the souls of their people... Good and evil... It consumed.

It grew stronger, endlessly mirroring itself within the space of my dream. Endlessly mirroring... Expanding... Infinite.

What it was before, it is no more. Neither beast nor god, it is a creation unlike all.

It is... The Swarm."

And heres the rest of the echo stones up for grabs if you need em to remember what I'm talking about: http://wiki.spiralknights.com/Artifacts#Echo_Stone:_Gloaming_Wildwoods

Now this is where I'm stumped. I can't say my full thoughts of this, as it contains SpiralSpy unreleased content, yeah, stinks I know, nearly got banned.

But its 1 of 2 things, the second is from Spiral Spy so I wont say it until it's released.
1. The Swarm is something made, but became twisted, thus consuming everything, then recreating it (such as Void Lumbers) into stronger beings.
2. [Unreleased Content cannot be shown on the forums]

All together it looks like the Swarm was originally a creation by something, probably not Tinkinzar, I'll say why.

The world is its prison.
Now that is the Echo Stone talking, meaning it is the CORE's prison. It says it used to be a place to merely protect it while in slumber, hence the core is a living being

Tinkinzar made the Clockworks to protect the core, for reasons unknown other than to protect it while it "slept" (hence the name Cradle) from said Swarm and other stuff.

And this is where I'm stuck. I could add the Swarm idea's I had and bring that into play, but as it wasn't released yet, I can't say any more about it specifically. Also It hasn't helped me anymore from this part onward.

Discuss. I'll update this as more info comes in and such.
All updates will be below this line
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Update 3/14/2012:

Yeah, update on the same minute I post lol.

Anyway one part I forgot to add was this.

In the very final missions out at this time, 9-3 to 9-4, one of the knights (Feron, Vaelyn, Kora. Forgot which) says that he/she had a feeling that the knights were meant to be on Cradle, as if something needed them.

So was the Core using it's Energy/powers/whatever to actually destroy Skylark and force us into this whole thing?

Think on that while I eat my soup... (litterally. I'm a soupaholic lol @_@)