At SongMeanings.com a user named _yoda writes:

When I saw The National live at the City Recital Hall in Sydney (first show), Matt remarked wryly just before the song began: “This is a song about love… between two brothers”.

The title is a reference to the story in Genesis. Cain is Abel’s older brother. Because God likes Abel’s sacrifice more than Cain’s, Cain becomes jealous and kills his brother. God asks Cain “Where is Abel?”, and Cain answers “I don’t know. Am I by brother’s keeper?”. God curses Cain.

The narrator of the song appears to be represented by Cain, who is out of control and asking his brother for help, sympathy, or something else.