Will Daenerys And Jon Split When The Truth Comes Out?
Sam's big reveal in the crypts at Winterfell didn't just shine a light on the different kinds of ruler that Jon and Daenerys would make, of course - the simple fact that Jon/Aegon has a claim to the throne has the potential to cause a huge shift in alliances, and even to end theirs. Since Jon bent the knee and they had their intimate moment on the boat in the season 7 finale, season 8 has been all about showing these two as a couple in love. "Winterfell" repeatedly showed them as a couple, with Jon even mounting a dragon and the two riding off into the icy wilderness together. Varys, Tyrion, and Davos spoke about the possibility of them ruling Westeros together, and even Sansa (who is far from Daenerys' biggest fan) throws Jon's love of her in his face.
However, given Daenerys' obsession with the Throne, and her willingness to do whatever it takes to get there, the reveal that her lover is also her potential rival may be enough for her to switch to seeing him as an enemy. This may not happen immediately, but especially when they are currently in the North, where support for Jon is strongest, seeing how the smallfolk love him may be too much for her.
In the early seasons, Daenerys was repeatedly assured that the common people of Westeros were waiting for her return, and would cheer her in the streets. However, now that she has arrived, they are far from applauding her, yet they appointed Jon to be King in the North. And should Jon and Daenerys split, it's clear who would be the hero and who the villain. Between the man who has never wanted power, yet sacrificed everything (even his life) to protect his people, and the woman who is a conqueror, happy to barbecue everyone in her way, there is simply no question.
Daenerys As A Villain Is Controversial, But Does It Make Sense?
As it stands now, Jon and Daenerys are the heroes, standing against both the Night King and Cersei (presumably in that order). At this late stage, taking Daenerys from hero to villain would be an incredibly controversial decision - but it may be the best way for the series to end. Most fans assume that the Night King will be defeated, and the final throwdown will be between human characters (although there's no guarantee of that happening!), but it may be just a little too obvious to have that be between Cersei and Jon/Dany. Cersei has been rising as a villain from the start - having her battle the ever-heroic Jon and his lovely rightful Targaryen Queen feels a tad too Disney for a show that prides itself on twists and turns. Both Jon and Daenerys surviving would also be a little too much of a happy ending (especially given that the ending has been officially described as 'bittersweet').
Having Daenerys turn into the villain, however, would be something that fits perfectly. This would also create a beautiful villain origin story. From her beginnings as an exile, dreaming of a return home, through her meteoric rise to Queen, and savior of her people, it would take this arc all the way back down to show how her grand ideas of freedom weren't enough to make her a hero. How an obsession with power, and a determination that she is 'right' in believing that the Throne is hers, is enough to take her from Mother to Dictator.
This also fits with the Game of Thrones lore about Targaryens - that they have a tendency to madness, one that Daenerys has definitely shifted more and more towards as her story continues. There would be a wonderful symmetry to have the death of the Mad King set the events of Game of Thrones in motion, only to be wrapped up by the ascension and death of a Mad Queen - and while this is far from the only way that the series could end, 'Winterfell' certainly sets it up as a serious possibility.