Rafael was a Shadowhunter born in the year of the Mortal War in Buenos Aires. During the Dark War, his home, the Buenos Aires Institute, was ambushed during a series of attacks, the perpetrator being Sebastian Morgenstern, with his Endarkened and fey armies. The boy was one of the few survivors of the attack on the Institute; his parents perished and their Institute was taken over by corrupt Shadowhunters, due to which Rafael was orphaned and ended up living on the street.
He found refuge at the local Shadow Market where he was at first cared for by a werewolf who took in children, prior to her disappearance,  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.
In early 2012, Rafael was found by Alec Lightwood and Lily Chen at the local Market. Rafael helped the duo find some missing werewolf women, informing them that he'd spied on corrupt Shadowhunters lurking around the Market. Owing to Rafael's inability to speak English, they communicated through Lily, who was adept at speaking Spanish. Rafael was skeptical about Alec initially, but he came to trust him 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 had kidnapped some werewolf women, Rafael bit Clive Breakspear when he threatened Alec's life, which resulted in him being knocked out himself. Tessa healed him, and, upon waking, he immediately asked for Alec. When the building collapsed with Alec still apparently inside, Rafael, distraught, wanted to charge in, but was stopped 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 his home in New York, and Rafael did not object. Upon his 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 later, the family Portaled to the London Institute, the parents going to aid the former inhabitants of the Los Angeles Institute. There, Rafael and Max befriended the youngest Blackthorn, Tavvy, and was won over by Cristina Rosales, with her Spanish lullabies.
He soon attended Livvy and Robert's funerals, where Rafe and Max tried to console Tavvy for the loss of his sister. When the bodies were set on fire, the siblings held each other's hands as they stood with their family.
Once Magnus started getting sicker due to the illness affecting all warlocks, he traveled to Los Angeles for possible treatment. Max and Rafe stayed in New York and were looked after by Simon and Isabelle, where Alec checked on them daily and asked after Max's wellfare.
While the rest of their family was camping out in Brocelind Forest in preparation for the Cohort's parley, the siblings, along with Tavvy and Dru, were watched over in Alicante by Maryse. Following them seeing the battle break out over the Projection, Rafe and Max were taken inside the Graymark house.
In October of that year, around three weeks after Alec's appointment as Consul, their family, friends and loved ones gathered at the beach by the Los Angeles Institute at what turned out to be Magnus and Alec's wedding ceremony. Though it was a surprise to Magnus, the rest of the guest had been informed and planned for it; Isabelle even having brought gold and blue outfits for Max and Rafe to wear. During the ceremony, Rafe appeared solemn—understanding the seriousness of it—but afterward joyously danced with his family.
- The Land I Lost
- A Long Conversation
- Lady Midnight (first mention)
- Lord of Shadows (first appearance)
- Queen of Air and Darkness
- Forever Fallen
- 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".
- Rafe is seemingly good at soccer when he concentrates.