What’s the difference between ‘why’ and ‘how come’? They have the same meaning but the nuance is different.
‘Why’ can sound like quite a direct question in some situations.
For example:
“Why did you come to Japan?” – It means, ‘give me a reason!’
It’s much better to say
“How come you came to Japan?” – It means, ‘please tell me more’.

‘How come’ is a softer, friendlier way of saying ‘why’.

Try it!