Within the hierarchy of angels from Christian mythology, Raphael is one of the four Seraphim, the highest rank. His name means "One that heals." He is said to be the guardian of the Tree of Life, opposite the Tree of Knowledge in the Garden of Eden. Most of Raphael's exploits take place in the Apocrypha, where he has roles as imprisoner of Azazel (an angel that gets exiled from Heaven for having sex with human females) and guide of Sheol, the Hebrew underworld.
Though he is not depicted as a lover of another being, Raphael is in the Lovers Arcana due to his appearance in the Lovers Tarot Card, and his status of the patron Saint of lovers due to his involvement of uniting Sarah & Tobias in the Book of Tobit.
"Origin: Israel. One of the 4 heralds, the seraph of wind. An angel with a gentle temperament who is said to blend in with humans and speak with them. He guards the tree of life in the Garden of Eden and rules over the cherubs."
—Shin Megami Tensei A-Mode DDS Dictionary
Along with Uriel and Gabriel, Raphael is one of the three major sub-bosses of the last arc of the game—the seraphims, and one of the most powerful angels under God's orders that stands guarding the superior part of the Basilica.
He appears defending the fourth floor, accusing the protagonist of being "covered in the blood of the righteous" before engaging him in battle in case he's not law aligned. This fight, however, is entire optional, as the player can choose to just take the stairs towards the next floor without having to enter Raphael's room.
In Law route, he instead joins the protagonist's party, as he is required in order for a triple fusion with Uriel and Gabriel can be performed, resulting in the creation of the "Angel Ring"—a valuable item needed for the final showdown against Asura to become available.
"One of the four major archangels. His name means "healer". He explains the history of the fallen angels and the creation of Adam and Eve."
—Shin Megami Tensei III: Nocturne Compendium
Raphael is encountered and fought in Mifunashiro if the Demi-fiend is against the Reason of Yosuga. He is fought along with Gabriel and Uriel. Following his defeat, he can be created by fusing a Dominion with Uriel.
The ability to fuse Raphael comes from completing the Blessed Light quest, where players with a Uriel summoned are asked by an NPC to defeat the Mad Avatar Raphael that regularly spawns in Shibuya by Celu Tower. He is a special triple fusion of Uriel and two Throne.
The true identity of one of the masked men at Kagome Tower. He reveals his true form at Shene Duque alongside the other three. He is fought in the DLC Challenge Quest Clipped Wings 2. During the battle, Raphael will ask Flynn if the situation fills him with melancholy. Answering no will cause Raphael to lose a Press Turn. Upon defeat, he will ask why Flynn, one of the chosen, is smiting the Archangels and wonders if he has the same 'unclean blood' as Aquila.
Raphael has the special power WindProof, which prevents death by wind attacks. Raphael can do the light based combo War Breath with Uriel, which increases the parties stats for 15 MP. Raphael can perform the combo Soul Eater with Dred Cat.
Raphael is a spy sent by Ose to keep track and sabotage the Devil Children's attempts at stopping Empra. He's also an inventor who tends to build machines that go out of control. He has a younger brother and sister named Zadkiel and Tabbris, and after becoming close with the party eventually betrays the Imperium once they threaten his family.
Raphael along with the other three archangels are optional bosses to be encountered before the party enters the airport. Much like the other archangels, Raphael is a human turned demon who struggles with recollecting his memory and his hunger, along with suffering from an identity crisis where he believes he is a Millennial Kingdom angel. Raphael resides in the interment factory in the same room where the party picks up the processed can used to weaken the Jailer.
Raphael specializes in using electricity and wind attacks in battle while boasting physical attacks that target the party. He also possesses Debilitate.