The ship is transporting a evil serial killer to a maximum security prison. During a hyperspace transit the ship is attacked by hyperspace demons or creatures that attack the minds of those awake and the crew have to drop out of hyperspace in an emergency - leaving them in a random place far from home.

They have to go back in to hyperspace to return home, the trouble is everyone will have to be in deep sleep but someone has to do the necessary functions to send the ship through hyperspace as it's not automated for safety.

For some reason the serial killer's mind was not attacked, he/she is missing the part of their mind that would make them susceptible. The only way home is to let them pilot the ship...whilst the crew sleep

Man, I wished you'd asked a year ago. I've no idea where my first Derelict Delvers draft with all this stuff is at the moment.

Every 100 years a rift opens in a sector bordering human controlled space and the Xixi an alien rival but this time the first manned ship sent into the rift 7 years ago returns empty but with evidence of something horrific and unexplained by any normal scientific explanation. The Xixi are on alert because they assume humanity has come up with a weapon they're unable to defend against.

That cargo you picked up on spec from the gypsy steamer for transfer to the mining colonies just started making a funny beeping noise. Upon investigation it is revealed to be several kilos of antimatter in a jury-rigged containment vessel, which you recognise as being not dissimilar to the one ComFedSec blew up a space station trying to recover a couple of weeks back, with the loss of scores of lives.

And hey, was that a screw that just popped out the side?

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The Dragarian Geocentrist mindwipers have been up to their old tricks, except instead of shanghai-ing innocent tourists from Plethora's purple beaches and turning them into genocidal zealots, this time they've gone and done it to your ship's AI. Unplug the droids!

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The ablative hull plating you were sold to keep the ravages of the Mist (stellar feature?) at bay appears to have been diluted with substandard alloys.

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A mini-nova blows out a large section of space, sending gaseous vapours flying hither and yon, revealing a previously unknown dead system of planetoids, all now scurrying randomly across space, containing hidden treasures from an ancient race of extinct aliens. Technological secrets, cultural artifacts, dangers, horrors and mysteries await those bold enough to join the scramble to explore them.

Alien spores tromped in on the boots of a stalwart crew member appear to have taken quite the liking to the ship's memory crystals.

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Space pirates no longer use dramatic stalk and strike tactics, instead they disable a crewman in a rough port and insert one of their own as a replacement. The saboteur works from within to sow dissent, before finally staging a mutiny. Or cuts the fuel lines, whichever is handier.

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Hypervelocity needledust from a conflict millennia old whips through important sections of the hull. Sir Isaac Newton is indeed the baddest motherfucker in space.

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Zombie-creating nanobots have somehow infested the ships medbay.

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Your ship enters a mysterious gravitational anomaly some have dubbed "the dragon's coil", that appears at random for no good reason. What this does is send the ship into a literal spiral, like a gravitational slingshot around an invisible, infinitely long trail which may be a condensed dark matter formation. Before too long, the ship will rupture from the centrifugal forces, unless a means can be found to escape.

Players are encouraged to talk like their faces are being pulled off in a centrifuge.

Whispers in the dark: the ship's resident ham makes a hobby of collecting decades-old transmissions from ships and crews long gone as they make their way across the lightless void, translating and decrypting them. This time however he runs in excitedly clutching a print of something new.

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You've accidentally wandered into a dead zone, where small scale electronics no longer work due to a quirk in the local laws of physics.

The group decides they want to deposit some of their earnings, gained after a recent adventure, in a high interest savings account. Locating the one with by far the best rates, the group sets off, but upon entering the system they discover they are being attacked by increasingly determined aggressors. Apparently someone deposited a small sum as a bounty on their heads in the banking system four hundred years ago.

This may lead to a discovery as to how the system banks can offer such attractive rates.

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The tattoo a crew member got on the last shore leave turns out to have a viral component.

Your crew finds a ship that is adrift and boards it.  On it they find humanoids (the crew and some passengers it would seem) that appear to be in suspended animation in their pods.  The control consoles for them are too alien to figure out.  The ship's interior looks way far advanced compared to your own ship.

****** SPOILER (maybe) **********

The humanoids are not in suspended animation.  They are not cryo frozen.  They are in stasis fields.  Time has completely stopped for them.  Further examination will reveal that they all show brain activity.  As if they are dreaming, or thinking.  But they can't move.

These are beings that come from a universe that has no time.  They have no concept of time.  Yet their active minds would make your crew think otherwise.  The aliens are fine as long as their stasis fields remain on... always.  They can't survive for just one wink of an eye or less of time.