Remus suffered great mental anguish as the war escalated when he learned that his wife was pregnant. He even tore out a clump of his own hair in anxiety over the possibility that his child would be born a werewolf. He visited Harry, Ron, and Hermione while they hid out in Grimmauld Place and offered to help with their search for Voldemort's Horcruxes. However, Harry denounced him, calling him a coward for even considering leaving his wife alone while pregnant. Remus left them greatly agitated.

Harry and his friends next heard of Remus on Potterwatch, under the code name "Romulus". Remus made Harry realise that they were still good friends, with his putting forth the opinion that Harry's instincts were good and they were usually right.

Remus eventually came to his senses and reunited with Tonks in time to see his son's birth. They named him Edward Remus "Teddy" Lupin, after Tonks' father, who had recently been murdered by Snatchers after refusing to turn himself in to the Muggle-Born Registration Commission. Appearing to forgive and forget their earlier disagreement in Grimmauld Place, Remus asked Harry to be Teddy's godfather.