The Earl of Sussex and the Lord Chamberlain begin the play by inquiring to each other which lords are present in conference with Queen Mary. Tame and Chandos enter and discuss the possible marriage between the queen and Philip of Spain. At this point, Lord Howard and Sir Henry Beningfield arrive and tell of how certain rebellions against Queen Mary have been promptly put down, and the offenders executed, before Bishop Gardiner arrives to summon all the lords to the queen's council chamber.
Queen Mary meets with a number of lords in her council chamber, triumphing over her recent victory over the rebels, when one lord, Dodds, inquires if he and his followers may still practice the Protestant faith that was the norm during the reign of Mary's brother Edward. The queen and Bishop Gardiner are extremely angry with this, and Dodds is sent to the pillory. Beningfield then reminds the queen that her sister, Elizabeth, may have something to do with the petitions and rebellions involving the Protestants that have been going on lately. After hearing this, Mary orders that Elizabeth be arrested and imprisoned in the tower, and Sentlow, another lord who is present, is also taken away for defending the princess. Yet another lord, the Earl of Devonshire (who is not present) is ordered by the queen to be arrested for supporting the Protestants. Finally, the Lord Constable arrives and informs all present that Philip of Spain has arrived at Southampton. The queen and her party excitedly go off to welcome him.
Gage and a gentlewoman are discussing the Princess Elizabeth's troublesome state of health and mind when the clown enters to tell them that a large force of men have arrived at the castle. Tame and Chandos enter with their orders from the queen to bring Elizabeth in for questioning. The gentlewoman informs her that the princess is too sick to travel, but the men insist they must take her with them. Princess Elizabeth appears in her bed, being tended to by the two royal physicians (who both feel it would be a risk for her to travel), and agrees to go with the two lords to see her sister the queen. As a compromise, the men will stay the night at the castle and head out early the next morning.
Queen Mary and Philip of Spain triumph in the new alliance between their two countries and set their wedding date for July 25. Philip wishes that Mary's sister Elizabeth will attend the nuptials but is informed that, for complicated reasons, she will most likely not be able to be there. Tame and Chandos then enter and inform the queen that, although Elizabeth is sick, they were able to transport her to court. The queen tells the lords to examine her sister for the crimes she is accused of while Philip pleads for Mary to treat the princess as she would her sister, and not a criminal, when thinking of possible punishments.
Princess Elizabeth laments her state to the few servants she has left before Gardiner and the lords enter to interview her about her supposed involvement in the Protestant rebellion. As hard as the men press her, Elizabeth refuses to give them anything that will incriminate her in any way and adamantly proclaims her innocence. Since the councilors cannot get the princess to admit anything (knowing that there is no real evidence to tie her to any rebellion), they leave in frustration only to return soon after and inform her that she is to be committed to the tower, under orders from the queen, and is to have only two servants to attend her. Despite several of the lords pleading for the virtuous princess, she is to be taken to prison, under heavy guard, early the next morning.
Three white-coat soldiers prepare for a long night of drinking as they await to take Princess Elizabeth to the tower early in the morning. They talk of how they feel it is wrong for sisters to betray one another and how the princess is being wrongly imprisoned. By the end of the scene, the men are surprised that they have talked all through the night and that it is now morning.
Gardiner and Beningfield discuss Elizabeth's sorrowful journey down the river to the tower, and the two men wish she would simply conform to the queen's desires so she need not face any punishment.
Princess Elizabeth prepares to arrive at the tower, and the lords present lament the fact that she will have to enter through the same place that traitors do, while at the same time realizing that they have a responsibility to obey the queen's orders. While in prison, the princess is treated poorly, given unkempt servants and made to sit on a stone. All the while, the lords feel sorry for her and wish the queen would relent. They also attempt to convince the constable to be more lenient with his prisoner, but he will not do so.
The scene begins with a dumb show of the lords, and even King Philip, convincing the queen to treat her sister with more kindness. When the dialogue begins, Gage is attempting to, once again, convince the constable to give up his harsh treatment of the princess. The constable outright refuses, saying it is both his duty to the queen and as a good Catholic to punish the Protestant Elizabeth. However, the lords arrive and inform the constable that the queen wishes the princess more liberties (the use of the queen's apartments, leisurely walks in the garden and access to her own servants). Though reluctant to allow these privileges, the constable has no choice but to obey the queen's orders. While the lords inform Elizabeth of her loosened terms of imprisonment, the clown and the cook, both of whom serve the princess, enter successively, beating away the soldiers who were assigned to wait on their mistress in their place. The constable chides the men for their actions and tells them it was he who assigned the soldiers to do their duties. However, the cook merely brushes off the constable, who is angry and looking to take out his revenge on the princess.
A boy brings some flowers to Princess Elizabeth, much to her delight, but is accosted by the constable, who thinks he is delivering letters to the prisoner. Despite the boy saying he has no knowledge of any letters, the constable orders him to be whipped. Bishop Gardiner and other lords arrive and inform Elizabeth that she is to be removed from the tower and placed in the custody of a certain gentleman of the queen's choosing, which she has no choice but to go along with.
Elizabeth's cook and pantler and three poor men await the passing of the princess so they may greet her and show her the love she deserves. When the princess, escorted by the lords, passes by, she gives the poor men gold, and bells ring throughout the city in her honor. Both Gage and Tame are happy the princess is being received so warmly by the people while Bedingfield knows that he is under orders from the queen. Elizabeth leaves the people with a Latin expression before being led off to Tame's house, where she will be staying for the time being.
Beningfield sits down in the chair of state, and his man, Barwick, helps him take off his boots. The clown enters and, when asked to help with the boots, pulls the chair out from underneath Beningfield instead. An angry Beningfield then beats the clown.
An Englishman and a Spaniard are engaged in a quarrel which ends in the Spaniard being injured and the Englishmen, through treachery, being killed. King Philip and the English lords then enter, and the king says the Spaniard shall be executed for his heinous crime (at Charing Cross, the place where the crime was committed). The lords then continue their lament for Princess Elizabeth (except for the constable, of course), and Philip vows to speak with his wife and convince her to treat her sister mercifully.
Elizabeth sits with a number of the lords and her faithful servants as she awaits her fate. The princess wishes to write a letter to her sister the queen to proclaim her innocence. Beningfield, who is now in charge of her, is hesitant about allowing her to write the letter, but Gage says he will deliver it and accept any consequences that come from it. After writing the letter, Elizabeth falls asleep and has an eerie dream where a group of friars attempt to kill her, and she is rescued by angels, who place a bible in her hand. When she awakes, Elizabeth finds that there actually is a bible in her possession. Beningfield and Gage return and the former wonders why the princess has written a letter that only provides excuses and does not ask for submission to the queen. Elizabeth responds by saying that the innocent need not plead for forgiveness, before Gage takes the letter off to the queen. After they depart, Beningfield reveals his hatred for the princess and how he will do anything in his power to destroy her and please Queen Mary. The clown comes in and informs the lord that Elizabeth is conferencing with someone in the garden. This someone turns out to be a goat, and the clown is soundly beaten, once again, by Beningfield for his foolish behavior.
Bishop Gardiner and the constable mix in a death warrant for Princess Elizabeth with a number of other state papers for King Philip to put his seal to and not even realize what he has done. The men give the papers to a reluctant Gresham to deliver. However, Gresham reveals the whole plot to Philip and the lords, who are all appalled by the deceitful actions of the bishop and constable. The king then says that Elizabeth shall be released from her captivity and brought to the queen's presence to serve her.
The clown sees Elizabeth's lady, Clarentia, going off milking, and the lady tells him that she would rather be a free milkmaid than a gentlewoman in captivity, like her mistress is. A gentlewoman then arrives and informs the two that the princess has been allowed back at court. Clarentia and the clown immediately rush off to meet her.
Elizabeth tells Gage that she is still suspicious her sister has bad intentions, despite the fact that she has summoned her to court. Howard then enters and tells the princess that her sister has offered to give her an audience later that evening.
Queen Mary summons Elizabeth to her presence and asks King Philip to hide while they speak alone. When the princess arrives she declares her loyalty to her sister and queen, but does not admit to any kind of guilt and refuses to submit when prompted to. In the end, the queen forgives her sister all trespasses and invites her to dine with her that evening. Philip is very happy at this news but tells Mary that he must go back to the continent for the time being to take care of some business involving his father. The queen is heartbroken that her husband must leave, but knows that it is essential. After they depart, Bishop Gardiner and Beningfield tell how they are not happy with the reconciliation between the two sisters and that, if Elizabeth becomes queen, the old Catholic faith will be completely abolished from England. Therefore, Gardiner, who is gravely ill, has lain down a plot to trap the princess by arresting one of her servants on a trumped up charge and implicating Elizabeth as an accessory.
Elizabeth's lady Clarentia tells Gage of a dream her mistress had that is basically a description of everything that has happened so far in the play and then tells of a dream of her own involving a wedding.
A dumb show ensues that portrays the departure of King Philip from England, as well as the funeral procession of Bishop Gardiner. Sussex tells of how Gardiner, even as he was dying, wished harm to the Princess Elizabeth. Beningfield enters and informs Sussex that Cardinal Pole, a staunch supporter of the queen's, is deathly ill, which is news that Sussex is not exactly distraught over. The constable then enters and tells the men that the queen herself is gravely ill, before Howard arrives and confirms the queen's sickness and the death of Cardinal Pole. With the queen dying, the lords set off to wait upon her.
Princess Elizabeth still feels her life in is danger when Sir Henry Carew enters with news that Queen Mary has died and that Elizabeth is now Queen of England. All present are overjoyed by the news, and the new queen creates Carew Lord Hundson for delivering the good news.
The clown is celebrating the accession of Queen Elizabeth by lighting a bonfire when he is reprimanded by Tame for showing such joy so soon after the death of Queen Mary, just as he did after the deaths of her father and brother. After hearing Tame's speech, the clown says he will wait until he gets further down the road before being merry.
All the lords play their own part in the coronation ceremony of the new Queen Elizabeth, and the queen shows kindness and mercy to them all, including the constable, her former enemy, who claimed he was only doing his duty under Queen Mary. The procession enters London where the queen is greeted by the Lord Mayor, who presents her with a bible. Elizabeth then ends the play by giving a speech that praises the bible and how it helped her survive some turbulent times during her sister's reign, before the procession moves on.