Rheagar served the Night's Watch in the order of Rangers. Commander Hoster Tully seemed to regard him with some affection, and while many of the more seasoned brothers found Rhaegar to be arrogant, his dragon (though small) earned him popularity among the Night's Watch's younger recruits.
When Danae Targaryen arrived at Castle Black with Grand Maester Orin in order to flee Westeros for Essos, Rhaegar expressed a desire to accompany her so that together they could take the Iron Throne for their house. Danae rejected him, reminding him of his vows to the Watch.
When Commander Tully died, Rhaegar was chosen as the new Lord Commander after a close election.
During a harsh winter for the Night's Watch, Rhaegar recieved blame for the appearance of Others in the Riverlands. He led a small host to meet that of King Damon Lannister outside of Harrenhal. Enraged at being implicated in the Riverlands' problems, he entered a war council of lords and called the King a "thief" and a "pretender on a dragon's throne," prompting the Damon to order Ser Clarent Payne to remove one of his fingers. Danae, who had become Queen, wrote to her cousin afterwards, addressing him as "The Nine Fingered Commander."
Devorn Thenn arrived in King's Landing to complain about the poor management of the Wall. When Queen Danae Targaryen learned that Rhaegar still lived, she told Devorn of his dragon and gave her consent to have him attempt an assasination, as well.
"I offered you [aid and] you refused... like the kind of arrogant fool House Targaryen is known for. I accuse you of being idle, and furthermore I accuse you of being utterly incompetent and useless. If you were half the commander you seem to think you are in your mad head, then none of us would be here planning on how to deal with the Others so far south in the Seven Kingdoms again. Fire and blood you claim, but from the wall I have only heard silence and stubbornness." - Damon Lannister
"Ryk felt proud to have Rhaegar as a leader. He trusted the man with his life and would do anything asked of him. There were still whispers from other men about the Targaryen's inability to lead, but Ryk just dismissed those as envy." - Ryk
"To hell with all the other bloody Targaryens, there is the last dragon." - Beric Storm
"He is a green boy, a Southroner with no knowledge of wildlings or how to fight them. He knows nothing of the danger that lurks in the Land of Always Winter. He thinks having a dragon gives him some sort of right to lead. And worst of all, he prattles on about that ugly iron chair of yours far too much for my liking... When winter comes in the form of my brother and his army, the Watch shall need a strong leader, with the knowledge an resources necessary for defeating the wildling host. Rhaegar Targaryen is not the capable leader the Watch needs." - Devorn Thenn to Danae Targaryen
Danae Targaryen, cousin
Alester Targaryen, cousin
Aeslyn Targaryen, cousin (deceased)