It has a rather neutral meaning. It shouldn't be too offensive, but you should also mention that you are genuinely surprised. You could also say, "What brings you here?", or "What brought you here?". These phrases automatically convey surprise in almost, always a positive way.

My initial thought was that it’s a perfectly appropriate, neutral expression to use. Then, I actually imagined myself as the “foreigner” in your scenario — this was not too difficult, as I’ve lived in various countries over the years. Anyhow, I had an insight. Since you seem like someone who would like to be as good a communicator as possible in your interactions, I’ll offer my perspective in the hope it may be helpful to you. It occurred to me that the question, while not rude in itself, could indeed be a bit disturbing in certain contexts. The reason is that “how did you end up” can suggest that the other person didn’t really plan to move to your country for a good reason, but just settled there by default, or even by necessity. The implication is that you don’t have a high opinion of your own country, and by extension, of the foreigner who “ended up” living there. The person you’re talking to has no way of knowing if this a foreign language issue, or if you really have such a low opinion of your own country and of him. I would also recommend against showing too much surprise — as it conveys the same message. I would suggest you think of his decision to come to your beautiful country as perfectly natural, and say something along the lines of “What is it you like most about this (not “my”) country… that lead to your decision to move here?”

I don't think that it is a bad question to ask. Foreigners understand that your English isn't perfect and probably would not take offense to that question. Probably a better way of asking the question would be: "What is it that brings you to my country"?

I think it is a matter of tone. I've read that a similar question, 'How did you get here?' is good opener to approach people at parties or gatherings, as it has an open answer, one can choose to answer it talking about transportation, or how they know the hosts, or what they did that day before coming, and so on. But, if someone said it as "How did *YOU* get *HERE*?", stressing the "you", it becomes a way to imply that that person is standing out at that gathering (i.e. because they are from a different class, race, gender, etc.), so it can make them feel unwelcome/uncomfortable. Similarly, if you used an accusatory tone like you would use if you found your ex inside your house, or a too surprised tone (like if you found your cat inside a cupboard), that would also make the question more loaded. So, overall, said with a smile and a neutral tone, without stressing certain words, seems like an innocuous question.