What it means
You say long story short when you're skipping the full soap-opera version and dropping the bit that actually matters. It signals there was more chaos in the background, but you're serving the bite-size recap. Long story short, we missed the flight means the saga was there, you're just handing over the headline.
Usage examples
"Long story short, we are not going to make it on time."
"Long story short, the car broke down, we missed the ferry, and we ended up camping in a service station car park."
"Long story short, she got the job, so the drinks tonight are on her."
"Long story short, the deal fell through and we had to start all over again."
"Long story short, Dan tried to fix the leak himself and now the kitchen's basically an indoor pool."
Where it comes from
It comes from the older phrase to make a long story short, which is recorded in English by the 19th century. Over time people clipped off the opening and kept long story short as a quick conversational shortcut for jumping past the ramble and landing on the main point.
