Benighted has two meanings – the one that you probably know (although I confess I thought it meant something else until I looked it up for this) is that it’s an adjective which describes someone who’s without morals or knowledge. There’s also a second older, and more literal, meaning which is to be overtaken by darkness – whacking the prefix ‘be’ on to the start of a word generally changes the meaning to making or causing to be, as in becalm or bedazzle. If you put the two meanings together then it all makes sense – if you’re short on morals or knowledge then you’re unenlightened, or in the (figurative, this time) dark.
The literal definition of ‘benighted’ has been around since the mid-1500s. Here’s a nice example of it in action from W.B. Yeats in ‘From The Tower’ (1928):
“Benighted travellers
From markets and from fairs
Have seen his midnight candle glimmering.”
(When I re-read that, the thought of seeing someone’s midnight candle glimmering made me giggle a bit, because I’m extremely juvenile and smutty. I’m sure you’re much more grown up than me though, and the thought never crossed your mind.)