The episode proper starts after a 4-minute recap of season 1.
It's London, 1532, and King Henry and Anne Boleyn are seen praying and receiving Holy Communion in church. In the next scene Queen Katherine is seen praying in a different church and Thomas More is seen praying as well. The next scene shows Thomas More in a crowded room talking to the Spanish Ambassador Chapuys. They discuss their own support and the emperor's support for Queen Katherine but Thomas More begs the ambassador not to give him the letter from the emperor. He does wants not want to do anything that provokes the King's patience.
As Thomas More enters King Henry's room, Thomas Cromwell leaves it. King Henry tells Thomas More about a petition he's received from the members of the House of Commons dealing with the cruelty of the prelates and the clergy. They want freedom from clerical rule. While Thomas More condemns clerical cruelty he does not agree with the king and tells him the Church is the permanent sign of God's presence on earth. However, when the king asks whether Thomas More will speak against him, Thomas replies that he will never do so in public because of his loyalty and love for the king.
The next scene sees the king enter parliament. The king presides over a tribunal judging cardinals who supported the late Cardinal Wolsey and the Bishop of Rome, i.e. the Pope against their own king and country. The king assures the members of parliaments that he is not out for personal gain but is doing his duty as a king. As the spokesperson for the clergy, Bishop Fisher refuses to acknowledge the king as the supreme head of the church in England for it would mean abandoning their unity with the see of Rome. A compromise is suggested where the king is Supreme Head of the Church and Clergy of England, as far as the law of Christ allows.
In Rome, the Pope discusses with Cardinal Campeggio a letter from king Henry, asking for an annulment as well as a letter from the emperor, on behalf of his aunt Queen Katherine, to prevent the annulment. The Pope casually suggests that someone get rid of Anne Boleyn.
King Henry watches Anne read and claims he has to possess her utterly. Anne however, tells him to wait just a little longer. He tells her he is Head of the Church of England and mentions her staying in the Tower, as every queen of England has done before her coronation. The king leaves and her father enters and they discuss the annulment situation. Resistance is based around Bishop Fisher.
At dinner, Thomas Cranmer is introduced to George Boleyn and Thomas Wyatt by Thomas Cromwell. They, of course, also discuss the bishop and archbishop preventing the King's marriage annulment.
The scene switches to Mr Roose, a cook by trade, who is bribed by George Boleyn to do something unmentioned involving poison.
Next, Thomas Cromwell introduces Thomas Cranmer to King Henry. Cranmer was the one who suggested that the annulment issue was theological rather than legal. King Henry appoints Cranmer his own personal chaplain.
Henry and Charles discuss Charles' marriage to his 17-year old ward, Catherine.
Anne is seen waking up next to a man, but it's not Henry, it's Thomas Wyatt, the poet and her former and apparently current lover. However, the next scene shows Thomas Wyatt sleeping alone, obviously dreaming.
Next day, Thomas is received by Anne and she reminds him that they were once true friends. Thomas introduces Mark Smeaton to Anne. He's a singer, dancer, musician and 'all-round genius'. Smeaton gives an impromptu violin performance. Anne enjoys it and seems impressed with him to the dismay of Thomas Wyatt.
The cook is shown putting the poison in soup. The soup is served to some clergymen, including Bishop Fisher as well as Thomas More, who does not eat the soup. Next, Thomas More is telling Henry how the clergymen died but not Bishop Fisher, who only ate very little of the soup because he was talking to Thomas More. Thomas More talks to Henry about the rumours that abound concerning the plot against the bishop. Thomas Boleyn is mentioned as one of the candidates and even the Lady Anne, which upsets Henry. He has a tantrum and lists a number of bad things that are apparently all attributed to Anne.
Thomas More tells Henry that if he were to turn a blind eye to these murders, people will assume they were done with the king's blessing.
At the Tower, Roose is shown being interrogated by Cromwell when Thomas Boleyn enters the cell. Roose does not tell who paid him.
In the palace, Anne finds out that linen is brought to Queen Katherine, who still makes the King's shirts herself. Anne gets into a fight with Henry about it.
At the Bishopric of Rochester, Thomas More tells Bishop Fisher, who's still suffering from the effects of the poison, that the king has agreed that poisoners are to be boiled alive.
Henry visits Katherine and tells her she has to stop making his shirts. They discuss their daughter Mary, who's ill, but the Queen declines Henry's offer to visit her and proclaims that her rightful place is by his side.
In the presence of Thomas and George Boleyn as well as Thomas Cromwell, Roose is boiled alive.
At a party at the palace, Charles Brandon is seen dancing and Smeaton dances with Anne. Charles and Henry discuss marriage, again, and Henry asks Charles to do something for him, and then whispers in his ear. Charles goes to visit Queen Katherine and tries to convince her again to stop resisting the annulment. Charles reports back to Henry that Katherine will obey him in everything except when two higher powers tell her otherwise, God and her conscience. Henry storms off and happens to meet Ambassador Chapuys. He tells him that he will do what he wants in England and the Emperor cannot stop him, not even by threatening to excommunicate him.
Charles and his young wife discuss the Queen. Charles promises his wife that he will always be true to her. They kiss and make love.
Henry has summoned Anne and suggests they go hunting. They may be gone for a while and when they return the third person in their relationship, i.e. Queen Katherine, will be gone. He tells Anne he's already given Katherine instructions to leave.
At Thomas More's home, he wakes up and tells his wife Alice about his nightmare of the beast, the antichrist.
Next day, Queen Katherine watches Henry and Anne leave. Cromwell then tells her that she is to be gone from the palace within the month. She states that wherever he will send her, she continues to be his wife. Cromwell then has to tell her that she has to return the official jewels of the Queen of England.
Katherine is shown leaving the palace while the spectators bless her. Amongst the spectators are Charles Brandon and Thomas More. Thomas More assures her there will be even greater crowds on her return to London.
Anne and Henry are seen enjoying a late, private supper when a servant enters. He brings a message of farewell from the queen, who asks about Henry's health. Henry repeatedly strikes the poor messenger, sends him out and them apologizes to Anne.
In the final scene, two conspirators, one of them Ambassador Chapuys, are seen and heard plotting to kill Anne Boleyn.