18 June 1996, Remus participated in the Battle of the Department of Mysteries and defeated a number of Death Eaters including their leader, Lucius Malfoy. He was one of the only three combatants to see the end of the battle unscathed, the others being Albus Dumbledore and Harry Potter, proving Remus' exceptional skill at duelling. During this battle, Remus witnessed and was devastated by the death of his last surviving Marauder friend, Sirius, who was pushed through the veil in the Death Chamber by a curse cast by Bellatrix Lestrange. Remus barely managed to prevent Harry from diving in after Sirius, who was already lost.

Shortly after the battle and the end of school year, Remus along with Moody, Tonks and Weasleys confronted the Dursleys at King's Cross station over their treatment of Harry.