Not sure if this has been done before, so apologies if it has. But say through some military luck, Mary Queen of Scots manages to regain her throne in the period 1568-1570, what would change? How does this influence the religious issues within Scotland? If Mary has managed to remove some, if not all of the opposition to her rule during the war, how does this influence her governing policy? And what potential consequences could this have for the two kingdoms of Scotland and England? Who might Mary marry, if indeed she chooses to?
You'd think Mary might have learned her lesson from two disastrous marriages, but she was a romantic type and she's only 26-28 and the succession isn't really secure with only one kid. Accusations of her being a spouse-killer will also impede her marital prospects. Would Bothwell being off in Scandinavia make getting an annulment easier or harder?
There'd be a lot of domestic opposition, both on the grounds of religion and the fact that those noblemen who forced Mary out will not want her back for fear of her taking vengeance. Moray, if still alive, will be difficult (and his relations with his half-sister are probably unsalvageable after the York Inquiry and his presentation of the Casket Letters), as will the Lennoxes ("she killed our darling Darnley").
If James VI is raised Catholic his chances of getting England are diminished- especially if anti-Catholic xenophobia is still stirred up by wars with Spain and Catholic plots to assassinate Elizabeth. Though if Charlie Lennox still dies young and Elizabeth refuses to acknowledge the Seymour kids of Catherine Grey then heirs are somewhat thin on the ground- there was some iffiness surrounding the Stanley claimants (descendants of Eleanor Brandon) IIRC (Margaret Clifford Countess of Derby was in disgrace for the last 17 years of her life after making comments regarding Elizabeth's marriage negotiations with Anjou/Alencon, her son Ferdinando had the Hesketh Plot- though obviously a 1568-70 POD will alter these things).
Though if he's savvy James VI could see the way the wind is blowing and convert to Protestantism, either in opposition to his mother or after her death.
Much would also depend on
how Mary's returning to Scotland- being released by Elizabeth (unlikely- I think Burghley and others were very suspicious of Mary) or being sprung by her supporters are very different scenarios. And obviously if English Catholics break Mary out of prison then there will be major consequences in England itself.