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In this chapter, there is very heavy rain during the first part of the meeting between Daisy and Gatsby. Then, after about half an hour, the sun comes out. I think this is sort of a metaphor for the way things are going between the two of them.
At first, things are very awkward and neither of them feels comfortable. This is reflected in the rain --it's gloomy.
But then they get comfortable with each other. They are acting more warmly towards one another by the time that Nick comes back. This is reflected by the sun coming out and the weather being nice.