Maltravers informs Mortimer Junior that both Edward and Lightborne are dead. However, he also reveals that Gourney has fled and may betray them. Mortimer threatens to kill Maltravers, who is showing signs of remorse, but eventually dismisses him instead. Mortimer then boasts that he “stands as Jove's huge tree” and thus has nothing to fear from anyone.
Mortimer's response to the news of Gourney's betrayal once again demonstrates how arrogant he has become: he simply cannot imagine that he himself might be in danger. His comparison of himself to a tree—a symbol repeatedly associated with royalty in the play—further highlights his overconfidence and ambition.
Isabella enters in distress, explaining that Edward III knows about Edward II's death and suspects her and Mortimer Junior of ordering it. Mortimer is unconcerned, but Isabella explains that her son has already gone to seek the advice of his council. At that very moment, Edward III enters, accompanied by several lords.
Even the news that Edward III suspects Mortimer of Edward II"s murder does not disturb Mortimer. By contrast, Isabella seems aware of the fact that her and Mortimer's luck has run out, saying that this is the beginning of their "tragedy." Meanwhile, the fact that Edward III has sought the advice of his counselors before confronting Mortimer signals that he will be a better rule than either his father or the Protector—at least in the sense that he is willing to listen to the opinions of the nobles.
Hailing Mortimer Junior as a “villain,” Edward III says he knows that Mortimer murdered Edward II and intends to have him executed. That way, Edward III says, Mortimer's “hateful and accursèd head” can stand “witness” to his crime. He also rebuffs Isabella's attempt to quiet him, saying he fears she is guilty as well. Finally, when Mortimer questions who dares to accuse him, Edward responds that his father speaks through him, “And plainly saith, 'twas [Mortimer] that murd'redst him.”
Edward III's warning that Mortimer's severed head will publically testify to his guilt draws on an idea that has recurred throughout the play: that violence can be a form of communication. Unlike Mortimer, however, Edward III does not rely exclusively on force to shore up his position. In fact, his declaration that Edward II is speaking through him in some ways vindicates the former king's preference for language over violence. As king, Edward III will presumably strike a balance between language and force in a way that neither Edward II nor Mortimer was able to do.
Mortimer Junior challenges Edward III to provide evidence, at which point Edward III produces the letter ordering Edward II's murder. Mortimer at first attempts to protest his innocence but, quickly realizing the situation is hopeless, he orders Isabella to be quiet, saying he would rather die than “sue for life unto a paltry boy.” Before he is escorted away, he speaks scornfully of “Base Fortune,” noting that “There is a point to which, when men aspire, / They tumble headlong down.” Resigned to his death, he is escorted away by guards.
Mortimer's ineptitude with words comes back to haunt him in the form of the order for Edward II's murder. Despite Mortimer's attempts to craft a protectively ambiguous message, no one is ever in any doubt about what the letter means. Since it is also written in Mortimer's handwriting, his downfall quickly becomes certain. In being exposed and executed, however, Mortimer regains a measure of the courage and bluntness that had initially made him a sympathetic character: his stoic acceptance of his fate and his refusal to beg for his life restore some of the dignity he lost by becoming a liar and murderer.
Isabella continues to plead with Edward III, begging him to spare Mortimer Junior's life. Edward, however, takes his mother’s pleading as evidence of her own guilt, although he admits he hesitates to think her “so unnatural” as to have killed Edward II. Nevertheless, he orders her to be imprisoned, even as she herself begs for death instead.
In weighing the evidence of Isabella's guilt, Edward III once more brings up the topic of her "unnaturalness." It is not simply that Isabella might have been involved in her husband's murder, but rather the fact that she has committed adultery that makes her threatening: in addition to giving Mortimer broad and unlawful authority over both England and Edward III, Isabella's affair could in theory have placed an illegitimate child in the line of succession to the throne. In a society based on blood lineage, this would have been hugely disruptive.
Isabella is escorted to prison as a lord returns with Mortimer Junior's head. Edward III then asks his attendants to prepare Edward II's hearse, and as he waits for them to return, he laments that he could not “rule” Mortimer's “accursèd head” well enough to prevent his father's murder. Eventually, the hearse is brought in, and Edward places Mortimer's head on it as he proclaims his own “grief and innocency.”
With Mortimer's death, order is finally restored to England and the monarchy. The relationships that threatened to destabilize the social hierarchy (Edward and Gaveston, Isabella and Mortimer) have been violently ended, and Edward III's actions so far have indicated that he will show proper deference to his counselors while also ruling with a firm hand.