When you literally run through some where, e.g.
I have run through the streets of London
it is quite clear what is meant.
At a slightly more figurative level one might say,
I will run through our procedures with you.
This is also clear. One is teaching another something quickly, as if to make their mind run through the information.
But if I were a pirate and I found a dead body, I might say
He's been run through with a cutlass!
Now, I know that to run through means to stab all the way through the body, but how has run through come to mean that?