Book Five of The Faerie Queene is Spenser's Legend of Justice. It tells of the knight Artegall's efforts to rid Faerie Land of tyranny and injustice, aided by his sidekick Talus and the timely intervention of his betrothed, the woman warrior Britomart. As allegory, Book Five figures forth ideal concepts of justice and explores how justice may be applied in a real world complicated by social inequality, female rule, political guile, and excessive violence. At the same time, as historical allegory, it retells a number of the most important events of early modern England, in particular the controversies surrounding the colonization of Ireland. An integral part of the larger poem, Book Five also stands on its own as one of the most challenging meditations on justice in English literature.

These paired Arthurian legends suggest that erotic desire and the desire for companionship undergird national politics. The maiden Britomart, Queen Elizabeth's fictional ancestor, dons armor to search for a man whom she has seen in a crystal ball. While on this quest, she seeks to understand how one can be chaste while pursuing a sexual goal, in love with a man while passionately attached to a woman, a warrior princess yet a wife. As Spenser's most sensitively developed character, Britomart is capable of heroic deeds but also of teenage self-pity. Her experience is anatomized in the stories of other characters, where versions of love and friendship include physical gratification, torture, mutual aid, competition, spiritual ecstasy, self-sacrifice, genial teasing, jealousy, abduction, wise government, sedition, and the valiant defense of a pig shed.

Book Six and the incomplete Book Seven of The Faerie Queene are the last sections of the unfinished poem to have been published. They show Spenser inflecting his narrative with an ever more personal note, and becoming an ever more desperate and anxious author, worried that things were falling apart as Queen Elizabeth failed in health and the Irish crisis became ever more terrifying. The moral confusion and uncertainty that Calidore, the Knight of Courtesy, has to confront are symptomatic of the lack of control that Spenser saw everywhere around him. Yet, within such a troubling and disturbing work there are moments of great beauty and harmony, such as the famous dance of the Graces that Colin Clout, the rustic alter ego of the poet himself, conjures up with his pipe. Book Seven, the Two Cantos of Mutabilitie, is among the finest of Spenser's poetic works, in which he explains the mythical origins of his world, as the gods debate on the hill opposite his Irish house. Whether order or chaos triumphs in the end has been the subject of most subsequent critical debate.