"How come ...?" is slang or informal language for "Why?"
BUT
The word order in the sentence is different for "How come".
"Why ...?" uses the interrogative (question) word order.
For example:
Why were you at the hospital?
Why did the stock markets go down?
"How come ...?" uses the normal word order.
For example:
How come you were at the hospital?
How come the stock markets went down?
