The boy was a Shadowhunter born in the year of the Mortal and the Dark War. During the Dark War, the boy's home, Buenos Aires, was attacked by Sebastian Morgenstern and his Endarkened and fey armies. The boy was one of the few survivors of the attack on the Institute and somehow ended up living on the street, starving and stealing food from mundanes to survive, frightened by his sightings of the Shadow World.
Some time in 2012, Alec found Rafael and, together with Magnus, decided to adopt him, naming him Rafael Santiago, using their hyphenated surnames for their children, and took him back home with them to New York. Knowing the Clave's desires to increase their ranks, Alec constantly worried that they would take Rafe away to be trained as a Shadowhunter as opposed to being raised by a Downworlder.
- A History of Notable Shadowhunters & Denizens of the Downworld
- Lady Midnight (first mention)
- Lord of Shadows (first appearance)
- Apparently, Rafael loves music, especially lullabies in Spanish, and enjoys dancing, hide and seek, and light-up sneakers.
- He is presumably named after Raphael Santiago.
- In Lady Midnight, Emma heard Alec call Rafael's name, but misheard it as "Raphael".