After the return of Lord Voldemort, Percy Weasley secretly joined the Order of the Phoenix. Taking advantage of his rise through the Ministry, he was given the task of relaying inside information about Minister for Magic Cornelius Fudge and his administration to the Order. In order to shave off suspicion from Fudge, Percy was forced to estrange himself from his family and maintain a facade of hatred towards the other Weasleys and their association with the Order. He continued this mission even after the Ministry publicly acknowledged the return of the Dark Lord. When the Ministry fell to the Death Eaters in 1997, Percy was promoted to Assistant to the Minister of Magic and took it upon himself to organize a mass break-out of wrongly imprisoned Muggle-borns, smuggling them out of the country. He was discovered in early 1998 and went into hiding with the Order; he made his true allegiance known to his family and reconciled with them. Percy fought in the Battle of Hogwarts, and although he survived the battle, he was grief-stricken of over the death of his father, Arthur, and nearly murdered the Imperiused Pius Thicknesse in rage.
Following Voldemort's final downfall, Percy was invited back to the Ministry by the new Minister for Magic, Amelia Bones. He became Head of the Department of Magical Transportation under the new administration and reconnected with his Hogwarts girlfriend, Penelope Clearwater. The two married and had two daughters; Molly, named after the Weasley family matriarch, and Lucy.