The White Walkers can still be the main antagonist even if he leaves the Night's Watch. After all, they are a huge threat to all of Westeros. Jon might think he can fight them better outside the Night's Watch, but they are constantly advancing and could target him specifically for leaving his post. Maybe they see him as a key figure in the coming war and want to eliminate him before he can gather enough strength to oppose them.
In some fanfictions, he might leave due to a love interest. He could meet someone who makes him question his vows to the Night's Watch. This person could be from a different region or have a special connection to him. For example, she might be a noblewoman with a hidden agenda, but Jon is drawn to her and decides to leave the Night's Watch to be with her and get involved in the political intrigue of the Seven Kingdoms.
The main antagonist could be Littlefinger. He sees the early alliance between Jon and Daenerys as a threat to his own schemes. He might try to manipulate events to turn them against each other. He could spread false rumors about Jon's intentions towards Daenerys' claim to the Iron Throne or vice versa. His sly nature and ability to play the game of thrones from the shadows would make him a formidable foe to their budding relationship and their plans for Westeros.
The wildlings might be his allies. After all, Jon Snow has had interactions with them before. They are fierce fighters and could fight alongside him against a common enemy.
It could be a powerful underworld lord who doesn't want Naruto to leave. This lord might see Naruto as a threat to his rule in the underworld.
An ancient and powerful Pokémon with the ability to influence Pikachu's mind could be the antagonist. It might see Pikachu's potential and wants to use it for its own dark purposes. By making Pikachu leave Ash, it can start to manipulate Pikachu more easily.
The White Walkers could be the main antagonists. Since Jon Snow has found a dragon, they might see it as a threat to their plans of taking over the Seven Kingdoms. They would try to kill the dragon and Jon Snow to ensure their dominance remains unchallenged.
Common themes in Jon Snow Night's Watch fanfiction include leadership. Jon Snow is often depicted as a leader within the Night's Watch, facing challenges and making difficult decisions. Friendship is also important, his relationships with Samwell Tarly and other members are explored. And the theme of identity, as he is a Stark but also a member of the Night's Watch, and how he reconciles these two parts of himself in different fanfictions.
The main antagonist could be a new character. For example, a powerful ninja from a rival village who has a vendetta against Konoha. This ninja could manipulate Naruto into leaving Konoha by spreading false rumors about the village. Then, he tries to use Naruto's power as an assassin for his own evil plans.
Maybe the main antagonist is a powerful figure within Konoha who doesn't want Naruto to leave and become an independent force. He secretly sends assassins after Naruto. When Temari gets involved, this figure also targets her. His actions are driven by his thirst for power and fear of Naruto's potential outside of Konoha's control.
It could be Dimitri himself. Since he left Rose pregnant, his actions are causing a great deal of harm and conflict in Rose's life. He might continue to be a source of trouble, like trying to avoid any responsibility or interfering in Rose's attempts to move on.