Sadly, Young Sheldon season 6's attempt to fix Mary and George's marriage appears to be an outright lie, and one storyline reestablishes the dark future ahead for the family. It's no secret that the Cooper parents' relationship has been on shaky grounds for several years. Between George's growing misery and Mary's obliviousness to it, the pair has had a number of big fights. Things, however, changed in Young Sheldon season 6, when they seem to rekindle their lost romance. Their new peaceful and in-love dynamic is so surprising that even Missy doesn't know how to handle seeing her parents being so nice to each other. Unfortunately, the last few weeks of blissful marriage for George and Mary aren't going to last very long.
Young Sheldon season 6, episode 6 is an effective reminder of the dark days ahead for the Coopers. In the outing, George helps Wayne, who is going through a difficult period after he finds out that his wife is cheating with his best friend. ThroughoutThe Big Bang Theory prequel's run, Wayne's marriage has been painted as the ideal marital bond — something that George also points out in the episode. This proves that infidelity happens even to the seemingly happiest of couples. So even if it seems like George and Mary's relationship is on the mend, it isn't difficult to imagine that he would still engage in an extramarital relationship in the near future. If anything, it actually feels that Wayne's story is a precursor to George's own cheating storyline.
Young Sheldon has created several TBBT plot holes because of its lax approach to storytelling. That being said, George's impending cheating storyline is something that CBS cannot avoid, simply because of its impact on Sheldon. According to the socially-inept genius, he caught his dad in bed with another woman when he was 13 years old. Since he's 12 turning 13 in the comedy's current year, there's a chance that George's affair could go down late in Young Sheldon season 6 or early season 7. In any case, considering the sensitivity of the matter, The Big Bang Theory prequel needs to start actively setting it up to give the narrative justice, and introducing Wayne's marital woes is a good way to begin that.
Interestingly, Young Sheldon has been setting up Mary's affair as well. In season 5, Youth Pastor Rob was introduced and not long after, the Cooper matriarch developed a crush on him, At one point, she even dreamed of actually sleeping with her younger colleague. CBS hasn't explicitly established if Rob also has feelings for Mary, but it's clear that there's tension between them. Because she was fired from church, however, their interactions have been limited in Young Sheldon season 6, but that doesn't mean that their evolving dynamic can't go anywhere. Medford is a small town; people hang out in the same places. If they can bump into each other at the local bowling alley, it can certainly happen again elsewhere.
For now, Mary and George's marriage is going well. It's uncertain until when Young Sheldon is planning to sustain it, but something is bound to happen in the foreseeable future that will be the catalyst for George's impending cheating arc. So while Missy may be uncomfortable seeing her parents all in love with each other, she may quickly come to miss this time when things get bad and then worse with the death of her dad.