It is 1572 and tensions between Protestants and Catholics are at fever pitch in Paris. Steven falls in with Hugenot activists and coincidentally the Protestant Prince Henri of Navarre (Hugenot) has married the Catholic Princess Marguerite de Valois, the sister of the King. As a result tensions are high. They learn of a plot which would be an echo of a prior Hugenot massacre which alarms them. There is much going around trying to find the truth, and Steven being a newcomer who knows nothing causes the Hugenot's to be confused as to who he actually is. Is he a Catholic spy? Is he telling the truth about being a traveller? Matters are worse when a high ranking Abbot is the spitting image of the Doctor, making Steven think he knows the Abbot (Doctor) and confusing his Hugenot friends as to his role.
A curious scene is where the Doctor went in the first episode. The Doctor heads off alone to visit the apothecary Charles Preslin and while there urges him in a direction of scientific research of which he had gained some notoriety. He tells Preslin of another researcher who is developing a microscope which could be used to validate the theory of Germs which Preslin had developed. What's curious is how the Doctor is all pious about not interfering with history, and here he is, uh, interfering with the path of scientific development. What's the Doctor's game?
And this issue, his piety of noninterference, is again a theme in this story. At the end, when the Doctor and Steven are reunited on the eve of St Bartholomews day, the Doctor sends Steven's friend Anne off to her Aunt's. Steven is enraged upon learning of the bloodshed (St. Bartholomew's Day massacre) and how all the people Steven had met (Gaspard de Coligny, etc) were about to die. Steven was especially angered over the very very likely death of his friend Anne. It is somewhat curious his especial interest in Anne, and they had spent a night or two together so perhaps there was more to the story than was shown on the screen. In any case Steven is so angered and disgusted he insists that he'll leave the TARDIS at the first moment they land.
Where do they land? In Wimbledon Common in 1966. Steven leaves and the Doctor wanders into a whimsy reminiscence and pondering of how his companions had all left him.
The Doctor : "My dear Steven, history sometimes gives us a terrible shock, and that is because we don't quite fully understand. Why should we? After all, we're too small to realise its final pattern. Therefore don't try and judge it from where you stand. I was right to do as I did. Yes, that I firmly believe. "
This is likely the first we've seen the Doctor to be Alone, and the sheer loneliness of his path despite his continually having companions. But this time alone is very short-lived as a young lady bursts into the TARDIS thinking she's found a Police Box and she has an urgent need to make an emergency call. But, no, this is no ordinary Police Box and the young lady proves difficult to shoo away. At which point Steven bursts back into the TARDIS warning of real Police coming towards them, also no doubt expecting to make an emergency call.
Alone for a few moments, now the Doctor again has two companions. Steven and this new young lady who happens to bear a resemblance to the lady they left behind in 1572 Paris. Hmmm, they wonder, is this new companion, Dorothea Chaplet, a descendant of Anne Chaplet?