Game Of Thrones Season 6: 8 Ways Battle Of The Bastards Will Be Different In The Books
7. It Might Be A Fight Against Stannis Instead
Although like in the show Jon rejects Stannis' offer of legitimisation, the pair do still share a mutual respect for another, and Jon even writes to Stannis to warn him of the treachery of the Karstarks. With that in mind, it's hard to imagine Jon riding into battle against Stannis, if the latter were to defeat the Boltons.
But if Stannis did defeat Ramsay, and then manage to defeat Roose Bolton as well (who is also still alive, and has remained behind with some of his own forces at Winterfell), someone would be needed to rule the North, and it's hard to see that man being Stannis. He's an outsider, for one, and also he has his eyes on a larger throne.
Part of the Grand Northern Conspiracy theory is that the Northern Lords are pitting the Boltons and Stannis against each other, causing one to be defeated and the other significantly weakened, so that they can then swoop in, defeat what's left, and reinstall a Stark - either Rickon or Jon Snow - as the Lord of Winterfell, and perhaps even King in the North.
If Stannis wins, then the Northern Lords could well make that turn against him, and after that circumstances could lead to Jon riding to Winterfell. Even if they don't, Stannis would be more likely to leave the North than hold it, given he wants the Iron Throne, and with Rickon alive you could place a Stark back in Winterfell, but given he's still a child, it's easy to imagine the Northerners rallying behind the skilled-swordsman son of Ned Stark.
It still seems likely that Jon will leave the Night's Watch once he returns in the books, and where else can he go but Winterfell? But in this situation, it's not to reclaim it from Ramsay Bolton, but to ensure a hold on the North, which would also be extremely valuable in the war to come against the Others.