After scrolling through the scenario room page, it can be said that there are several storylines running throughout the clockworks, though some leave us hanging as to what happens.
Please add more and expand the storyline!
Caution: SPOILERS!
http://forums.spiralknights.com/en/node/36680
Here are some ideas.
CANDLESTICK KEEP:
-A small, thin four way junction, the two paths on the sides lead into two candle-lit rooms, both of them libraries with many bookshelves; the upper path, which leads ahead, has two gates in the way. The leftmost one has a Pepperkat, Bloogato, Statikat, and Hurkat lurking inside, along with a switch for one gate and four treasure boxes. The rightmost one has a book on a pedestal. Reading it the first time will trigger a conversation.
BOOK: "The kats are overrunning our defenses. We thought our magic would keep them away, but... (You notice something, and stop reading the book.)"
After this, the book will be unreadable while you fight two status-themed Zombies. Defeating them allows you to read the book again.
BOOK: "The kats are overrunning our defenses. We thought our magic would keep them away, but they seem to be deflecting it away. I have a feeling this will be the end of this section of the academy. That fool... (You notice something, and stop reading the book.)"
After this, the book will be unreadable while you fight two status-themed Kats and a Howlitzer. Defeating them allows you to read the book again.
BOOK: "The kats are overrunning our defenses. We thought our magic would keep them away, but they seem to be deflecting it away. I have a feeling this will be the end of this section of the academy. That fool Darkfeather cast a curse over the entire place, and it's so blasted dark I can't see them coming. Hopefully this candle will keep them away from (The sentence abruptly ends there, and you notice a few feathers scattered on the ground.)"
Two Owlite Feathers will appear on the ground, but beware- a Carnavon and two Kats will attack! Once these are killed, the other gate will open, allowing knights to exit.
COOLING CHAMBER (Tier 3):
-Cryogenic tanks with Swarm-infested monsters frozen inside them line the walls of a twisting, block-filled hall. A skull module (like the one @ a Danger Room) will say: "WARNING! Monsters are quarantined here. Tanks are very fragile. Do not break- monsters are Swarm-infested, will kill you on sight!" Hitting the tanks will shatter them, freeing the monster inside. The tanks hold Void Lumbers, Void Thwackers, Void Gels, Void Zombies, and Void Wolvers. To make matters worse, the area has four spawning Silkwings. Fortunately, Mist Gates on the side will keep enemies out. There are eight treasure boxes scattered in the room, so move carefully.
BLAST FURNACE (Tier 3):
-In this room, you can see a small floor below where Slag Guards are marching. One Slag Guard will appear in the area; a Freeze pot will spawn, available for use. The Slag Guard is accompanied by two level-specific enemies (Ash Tails, Oilers, Scorchers, Hotrodes, Slag Walkers, or Firebranders), scattered Shadow Fire, and a few flame jets in the walls, so be careful! Six Treasure Boxes will be awarded for killing the Slag Guard (by opening up a side room with the Boxes in them).
POWER COMPLEX (Tier 3):
-In this room, a strange machine will fire out supercharged Quicksilvers that splatter when they're done being charged. The area also has two Electreants (shock Lumbers) and four level specific enemies (other than Quicksilvers). Hitting multiple Ghost Blocks across a pit on the side will open the way to a switch that disables the machine and opens up a room with six Treasure Boxes.
WASTEWORKS (Tier 3):
-Knights may choose to descend up a long sloped spiral to reach a Party Button in front of a pipe. At this Party Button, a ! module will warn: "Releasing switch unloads caustic waste pipe #44 into drainage area; blockages will be automatically placed. Proceed with caution." Hitting the button causes acidic waste to begin flowing out of the pipe. The torrent of waste will trickle down at a pace Knights can outrun; however, it goes through walls. You will have to hit ghost blocks that suddenly appear; pots will be provided. If you escape alive, a treasure room will be open with eight Treasure Boxes; if you are hit, you will take heavy damage and be poisoned while inside the waste. After the waste reaches the end, it will begin pouring off the side; after it's been pouring off the side for ten seconds, the waste will be all gone.