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Raphael was a resident of Kirith. As a boy, he was known as a troublemaker, playing pranks and generally misbehaving. When his parents died, he became a ward of Miríl. He was a friend of Darien, but when he was taken away by the Panjistri, the zavát made Raphael forget all about him.
Ten years later, memories of Darien started to return, greatly disturbing him. One day, he went to the shore to think, but a storm broke and he accidentally fell into the sea. He was rescued by the Seventh Doctor and Ace, who had just arrived on Kirith. They returned him home. The next day, having fully recovered, he befriended Ace despite being told by Lord Huldah to avoid the strangers. After telling Ace about his memories of Darien, she decided to help him learn the truth.
Ace convinced Raphael to investigate the forbidden Harbours, where they discovered the laboratory where the Homunculus was kept, and were confronted by Lord Reptu. Fleeing, Raphael first went to Revna for help, but left angrily when he realised that it was she who betrayed them. He then went to the Doctor and Miríl, but all three of them were captured by Huldah. While the Doctor was taken to Kandasi Island, Raphael used Ace's nitro-9 to free himself and Miríl and was reunited with her. He argued with Arun against killing the Homunculus, but was forced to kill it himself when it broke free and attacked Ace.
After helping to convince Tanyel of the truth, Raphael, Ace, Arun and Miríl set out to Kandasi Island; during the voyage he was devastated by the death of his mentor. They reunited with the Doctor at the island and teleported themselves to the real Kandasi, where they learned that the Kirithons were part of the Panjistri's plan to create the God Machine. While the others went off to rescue Ace from the Grand Matriarch, Raphael was telepathically drawn to the God Machine and joined with it, his recent experiences making it complete. (PROSE: Timewyrm: Apocalypse)