Imperial Ships are massive structures. Light Cruisers, like the Valkryie, are roughly between 4 and 5 kilometers long, .5 to 1 kilometers tall, and .25 to .75 kilometers wide.
The smallest light cruisers (4x.5x.25) have 500 million cubic meters of space. Cruisers can have more than 3.5
billion cubic meters of space. This block (the whole block, not each piece) is 1 cubic meter:
http://upload.wikimedia.org/wikipedia/commons/0/02/Metre-cube-beton-p1040192.jpgMuch of this is taken up by the plasma drives, the engines, the cargo hangars, and the crew quarters. However, it is such a massive amount of space that there are often voids. A level of the ship might become disused or even abandoned all together.
Say the plasma drive leaks onto one of the less used subdecks (we'll call it Happy Deck A-3) and radioactive sludge washes through a couple of rooms and the hallway. Do you send in dozens of guys in special suits to gather it up, move it through the ship, and eventually reach a place where it can be safely vented in space? Hell no, that risks spread the crap to the rest of the ship. Best to just lock the door and forget that Happy Deck A-3 was ever there. Didn't get used much anyway, the pump workers on A-4 just took their smoke breaks there. Speaking of which has anybody seen Phil and Andy?
Happy Deck A-3 is now a Black Deck.
Black Decks are parts of the ship where no one goes, for one reason or another. It might have been a spill, like above. It might have some fault, like the air pumps don't circulate there anymore. Sometimes they are literally just forgotten about by everybody else on the ship. Whatever the reason, Black Decks are the dark underworlds of an Imperial Ship. Monsters grow there, things which escape other parts of the ship move there and either die or thrive. Convicts (because with 50,000 people sharing elbow room you have to have a court system), criminals, and crewman who just get tired of working for "the man" sometimes run away into the Black Decks and disappear. They might survive if they can deal with the intermitant power issues, the radiation, chemicals, and the monsters. Infact, they might get better, learn to see in the dark and grow claws or bigger teeth to catch their meals.
All ships have Black Decks to varying degrees. It's a simple fact of space fairing life.
It also, on occation, happens that something long forgotten is needed, and must be recovered from a Black Deck, or that crewmen who happen to be statoned near a Black Deck begin disappearing. In these cases, action is called for.