Widower and single father Thomas Farriner is the king's baker, currently providing the Navy with bread and biscuits from his Pudding Lane bakery. His sister-in-law Sarah often helps out at the shop - a distraction from the fact her wayward husband (Thomas's brother) has been missing at sea for months now. Thomas is dismayed to learn from Navy official Samuel Pepys that it's unlikely he'll be paid for his latest job, owing to the expense of the war against the Dutch. However, he instead sends the baker away with a letter that could be the key to Sarah's closure. Meanwhile, in the palace of Whitehall, the king attends a stately dance, where an attempt on his life is foiled. Later, Thomas returns to find the bakery ablaze, with his two daughters asleep upstairs.
As the fire begins to gain strength, Thomas breaks his way into sister-in-law Sarah Farriner’s lodgings to wake the family and lead them to safety. Sarah is nowhere to be seen though. Thomas leads the rest of the family through the crowds to the Thames. before they make their way north towards Moorfields. Sarah is being held in a private cell at Newgate Prison while Denton quizzes the Duke of Hanford’s Footman.
Thomas makes a return to the city in search of Sarah to see the fire spreading at an alarming-speed. Elsewhere Sarah sneaks back into Hanford house and retrieves the mysterious box form Senor Romero's room. She later comes face-to-face with Thomas, she attempts to warn him away and she leaves Thomas confused and hurt. Denton moves towards to the palace, where he is interrupts a meeting between the King, Romero and James. Denton accuses them of treason. James denies this. Elsewhere, Elizabeth confronts Pepys about his infidelity. Thomas finally finds Sarah on the streets, hiding from Denton's men.
King Charles finally takes action as the fire creeps closer to the Tower of London; Sarah is recaptured; Thomas seeks Pepys' help to influence the king.