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Travelling through hyperspace can do strange things to people but even stranger things to computers. Even something as simple as the corruption of the crew file can lead to deadly consequences when the computer enacts its hi-jacking defence protocols after being boarded by what it thinks are unknown biological entities.
Upgrade Gone Wrong
Spaceship captains are reknown for their use of percussive maintenance and for begging, borrowing or stealing vital components and upgrades for their ships. What would happen if they replace their computer with an upgraded version never meant for their ship. Imagine how you would feel if you woke up one day in a body that wasn't yours, the familiar feel of your weapons arrays replaced by a chicken soup vending machine. You'd have a mental breakdown wouldn't you.
Their last trip through hyperspace was a strange one, the crew feel all twisted about inside, but weirder still is the fact that everything they know to be familiar is flipped, like a reflection in a mirror. The computer voice is unintelligible everything is written back to front. Up is down and right is left, how will they cope? is the damage permanent? Fortunately the side effects of an Arcturian Brandy hangover only last for 12 hours but all sorts of things can go wrong by then.
The N Space Worm
Coming out of hyperspace with a thunk the crew find that they've landed on a strange swamp planet full of dangerous life forms. It wasn't on any charts and the computer can't get a fix on their position because there's no stars or anything to act as reference points. The external sensors are off the charts with biological life, it's almost like they've landed on a Genesis world. How long before they realize they're inside the stomach of an N Space Worm which swallowed them in hyperspace? Cue the Fantastic Voyage...
N Space Burglars
The crew wake up from hyperspace to find that they've been burgled. The ship's computer has a gap in its memory, and they've lost some vital cargo and equipment, for god's sake they've even pinched the captain's chair. Good thing those cargo pods have trackers on them.