We have come up with a number of theories why Benjen decided to join the NW. One of the most common is that he had a role in R+L=J.
The dragon prince sang a song so sad it made the wolf maid sniffle, but when her pup brother teased her for crying she poured wine over his head.
The first sentence we have of Lyanna, Rhaegar and Benjen in it, and there is wine involved.
Benjen laughed. "As I feared. Ah, well. I believe I was younger than you the first time I got truly and sincerely drunk."
Benjen is telling this to Jon, Rhaegar and Lyanna's son. I think Benjen was staying at Harrenhal with Lyanna waiting for Brandon to come by, and pick them up on his way to his wedding to Catelyn Tully. As everyone knows, Rhaegar came by and likely poured his heart out to Lyanna, and they eloped. Lyanna likely left it to Benjen to tell Brandon when he came by what happened. When Brandon came by it was at a bad time as Benjen had gotten drunk for the first time. Brandon got some garbled info out of a drunken Benjen, and came to the conclusion that Rhaegar had kidnapped Lyanna. That led Brandon to go to KL, and kickstart the events that led to Robert's Rebellion.
Benjen blamed himself for the deaths of his father, brother and sister and the war, and that is what led him to take the black.
Edited by Fire Eater, 13 December 2013 - 11:13 AM.