In season five, during the selection of the new Lord Commander of the Night's Watch, Jon tells Sam about Stannis Baratheon's offer of legitimization. Jon confesses he's always wanted to be Lord of Winterfell, but tells a dismayed Sam he plans to decline the offer. So when Maester Aemon asks if there are any more candidates planning to run, Sam submits a nomination for Jon and gives a speech about his friend's heroism during the mutiny at Craster's Keep and the wildling attack. Sam's show of faith results in a win for Jon and deepens their relationship as confidants.
Later the same season, Sam learns from Stannis Baratheon that an abundance of dragonglass may exist on Dragonstone. Although still unsure exactly how the substance kills White Walkers, this news (coupled with the death of Maester Aemon) prompts Sam to ask Jon, his new Lord Commander, for permission to travel to the Citadel in Oldtown. Sam argues that the best way for him to help the brotherhood is to study and replace Aemon as the new maester of the Night's Watch.