It's not clear based off the context which the person asking the question means, due to simple ambiguity. By the rest of the conversation, it may be more clear, but it's not inherently obvious if, say, they tried starting a conversation with "夏休みに国へ帰りますか", if they are talking about when you want to return to your country, or were asking what you're doing over your summer.
To make this clear, you could simply add は in the appropriate place.
It's obvious here that they're asking "are you going back to your country in summer specifically", therefore making the more likely conversation:
I feel that this is actually the more natural of the two conversations. The fact that the questioner mentioned going back to your country, it just seems less likely that they're asking what you're doing over summer, which would probably have just been better asked by a 夏休みに何をする／どう過ごしますか etc.
Overall, you can't be certain without knowing the tone or ammending the grammar for clarity, but it seems much more likely that they're asking when you're going home rather than what you're doing over the summer, based off context, and the way in which the questioner is asking.