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; because his parents perished and their Institute was taken over by corrupt Shadowhunters, Rafael was orphaned and ended up living on the street.
He found refuge at the local Shadow Market where he was at first taken care of by a werewolf who took in children before she disappeared,  leaving Rafael starving and with little choice but to steal food from mundanes, or fight for scarce supplies at the Market, to survive.  There were times when his sightings of the Shadow World frightened him.
Early in 2012, Alec found Rafael at the Market. Rafael helped the pair find the missing werewolf women, informing them that he'd spied on the corrupt Shadowhunters lurking around the Market. Though Rafael spoke no English and understood little of it, they communicated through his companion, Lily Chen. Rafael was at first distant, but he came to trust Alec and found comfort in his hold. He was also fascinated by the man on the photos in Alec's phone, his fiancé Magnus Bane.
At the den of the warlock who'd kidnapped the werewolf women, Rafael bit Clive Breakspear when he threatened Alec's life and was knocked out himself. Tessa healed him, and, upon waking, he immediately asked for Alec. When the building collapsed with Alec still apparently inside, Rafael was distraught and wanted to charge in, stopped only by the others. The pair happily reunited when Alec emerged alive and well from the wreckage.
Alec, intent on adopting and caring for Rafael, asked him to join him home in New York, and Rafael did not object. Upon arrival, Rafael became immediately attached to Magnus and begged them to keep him. The couple agreed to adopt him, with their son Max quickly warming up to him. Magnus suggested giving him the second name Santiago, after his late friend with the same name. For months after, Alec and Rafael Portaled back and forth to Buenos Aires to finalize the adoption.
Some months after, the family Portaled to the London Institute, their parents going to the aid of the former inhabitants of the Los Angeles Institute. There, Rafe and Max befriended the youngest, Tavvy, and Rafe was won over by Cristina Rosales with her Spanish lullabies.
- The Land I Lost
- A Long Conversation
- Lady Midnight (first mention)
- Lord of Shadows (first appearance)
- Queen of Air and Darkness
- Apparently, Rafael loves music, especially lullabies in Spanish, and enjoys dancing, hide and seek, and light-up sneakers.
- His second name is for Raphael Santiago.
- In Lady Midnight, Emma heard Alec call Rafael's name, but misheard it as "Raphael".