Each of the remaining major characters in Game of Thrones has a pivotal scene that has changed them from who they were at the beginning of the show to who they are leading into the final season. This scene for Jon Snow comes at the end of episode 3 in season 6.
The Lead Up
Throughout season 5, Jon has been making lots of choices that people disagree with, but he’s put his honor before everything else. Right before he’s elected Lord Commander of the Night’s Watch, Stannis Baratheon offers him the chance to be legitimized as a Stark, so he brings the North to side with Stannis. Although it’s everything Jon has wanted for most of his life, he refuses because it would force him to break his Night’s Watch vow.
After becoming Lord Commander, Jon is faced with a number of challenges that he handles differently than other Lord Commanders might. The first is the execution of Janos Slynt. Jon decides to send Slynt to one of the other castles on the wall, but Slynt refuses. Once he’s on the chopping block, Slynt begs for mercy, but Jon knows whether he executes him or not, will define the way the Night’s Watch feels about him. He chooses to execute him to show his strength and commitment to the Watch.
The Unpopular Plans
While he was a prisoner/fake wildling, Jon learns the real threat from the North — the White Walkers. He makes the decision to go North of the Wall and offer safe passage to all of the Wildlings to prevent them from turning into more soldiers for the army of the dead. Since the Night’s Watch has long believed its job is to fight the Wildlings, few support his plan.
He’s successful in rescuing some of the Wildlings after a fierce battle with the White Walkers that saw him narrowly escape the massacre. But he keeps his promise to the Wildlings he was able to save and allows them get south of the Wall and gives them land to build their homes upon.
Life and Death
The members of the Night’s Watch who disagree with Jon’s decision trick him into a trap where they kill him by stabbing him repeatedly. If this were like most other Game of Thrones characters, Jon would have stayed dead. But he obviously has a bigger role to play in the larger story. Melisandre successfully brings Jon back to life the same way Thoros of Myr had brought Beric Dondarrion back multiple times.
After being brought back, Jon realizes that even when you make the right and honorable choice, you can still be punished by it. In the beginning of season 6, episode 3 he says:
I did what I thought was right and I got murdered for it.
After Jon is brought back, it becomes clear that those who murdered him must be executed, though Jon is not happy about the prospect, especially with Ollie, a young boy who had been serving as Jon’s steward and who had struck the killing blow through Jon’s heart. During the scene, right before the execution we can see him battling with himself in his mind. But after he does finally execute the traitors, he realizes that the Night’s Watch, the order he had served in for years and the order he was so proud to be a member of was not at all what he expected or hoped it would be. It’s a life-changing realization that no matter how much good is in the world, there will always be enough bad to swallow it.