And in the morning I'll be with you
But it will be a different kind

from Bon Iver – Skinny Love Lyrics on Rap Genius

Meaning

He is still there and the relationship continues but the feelings are not the same

This may reference the internal conflict with love that the speaker faces. At night, the speaker may want to end the relationship and feel very dark. but in the morning, it’s a new start, making it a vicious cycle. The speaker also recognizes that this love is a different kind because it is not pure or pursued with the best motives.

The relationship is built on sex of great passion and intimacy, which is not repeated outside of the bedroom.

After explaining what he needs from her to help him heal, he uses In the morning as a metaphor for what will happen after he is done recovering from his dark period (the night). It in the second line refers to the relationship, It will be a different kind of relationship, presumably a better one.

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