Some TMNT stuff really isn't for little kids.
In the IDW continuity, Raphael, like his brothers, is one of the reincarnated sons of Hamato Yoshi, who in medieval Japan were murdered by Oroku Saki. He began his new life in the present as a young turtle in the laboratory of StockGen Research, Inc., Baxter Stockman's genetics laboratory and served as a guinea pig for an experiment to be grown to be a naturally armored super soldier. Some ninja tried to seize the Turtles and various other research results from the laboratory, including a mutagen. The intervention also led his reincarnated father, now a lab rat, and the Turtles to be doused with a chemical cocktail that triggered their mutation.
Shortly before his mutation Raphael was, however separated from his family, by the attack of a hungry street cat. He panicked as he mutated and was taken under the wing of a homeless man named Buck. However, Buck was murdered by some street thugs, inspiring rage and grief in Raphael.
In the fifteen months after his mutation he eked out a miserable existence as a vagrant on the streets of New York City without a memory of his life before his transformation, or even of a name. During this time, his brothers regularly searched for him, but did not find him.
This changed on the night when he was befriended by Casey Jones after saving Jones from a beating by his father. During an attack by Old Hob, the other Turtles intervened, and brought an uncertain but happy Raphael home to Splinter. He trained extensively with them for the next month, making incredible progress and being rewarded with a pair of sais at the end of it.
Despite joining his brothers in their training and patrols, Raphael maintained his friendship with Casey by sometimes going out and assaulting criminals.
His new family's status was soon put to the test when their home was attacked by M.O.U.S.E.R. robots and Splinter was abducted. Raphael fought alongside his brothers to get their father back, but came to the attention of the Shredder and the Foot Clan in the process.
When Casey was badly beaten by his father, Raphael lost his temper and set out to murder the man, but was stopped by Splinter, who taught him that he fights with too much anger.
However, his anger was turned inward during the City Fall storyline, in which the rescuing of a stabbed Casey from Shredder led to Leonardo being captured and brainwashed into Shredder's second-in-command. Devastated, Raphael blamed the entire event on himself, and set out to savagely beat information on the Foot Clan from informants until Michelangelo and Donatello stopped him. When Splinter and the Turtles tried to extract the brainwashed Leonardo from Shredder's clutches, Raphael managed to penetrate some of the brainwashing and remind Leo of who they were.
At the O'Neil Farm in Northampton, Raphael clashed again with the emotionally-disturbed Leonardo, until Leonardo physically attacked him. From then on, Raphael watched and guarded his brother from a distance; including keeping Alopex away from him but did not engage him. He became more friendly with the mutant fox Alopex, though any trust he had for her was still shaky and he incorrectly believed that she had betrayed them when the Foot attacked.
Due to Hob's early efforts to kill him, Raphael remained extremely wary of Old Hob and didn't believe that their family should be working with him. Despite this wariness, he still went on errands to Hob on Splinter's behalf.
During the Turtles in Time event, Raphael was captured by Utroms in prehistoric times, and adopted a small dinosaur he named Pepperoni. When Leonardo attempted to change the past by killing Oroku Saki in medieval Japan, it was Raphael who talked him out of it.
He participated in the attack on the Technodrome along with his brothers Leonardo and Michelangelo, where they fought Krang. However, he was devastated upon returning back to New York, where a dying Donatello was barely saved by the Fugitoid by being transferred into the body of the robot Metalhead. Raphael remained convinced that Donatello was not really "alive," and that the Fugitoid wouldn't be able to save his life. In particular, he blamed himself for leaving Donatello behind.
When Splinter entered his family into the Gauntlet, an ancient ritual that would end the bloody conflict between them and the Foot, Raphael was pitted against the powerful but dimwitted Rocksteady, who had nearly beaten Donatello to death. He and Michelangelo used their skill and agility to pit Bebop and Rocksteady against each other. He participated in the final fight against Shredder along with his brothers, with his father as the victor.
When his father became leader of the Foot Clan, Raphael reluctantly joined as well, though he remained somewhat distant from it compared to Leonardo. He also remained in contact with their newly-estranged brother Michelangelo, assuring him that he knew how hard it was to be homeless, and that Michelangelo would always have a home with them.
The brothers reunited for a trip to Burnow Island shortly thereafter, where they encountered a mysterious alligator mutant named Leatherhead. Raphael and Leonardo also sought out two of Krang's remaining warriors, Tragg and Granitor, only to be knocked out by Leatherhead. They pursued the alligator to New York, but lost him.
Upon returning home, Raphael and his brothers were horrified to see Kitsune about to kill Splinter, and a brainwashed Alopex assisting her. Kitsune ensnared Raphael's mind and turned him against Leonardo.
Raphael attempted to reconcile Michelangelo with his family in the Chasing Phantoms arc, in which he argued that Michelangelo should be with them, even if their new place was as part of the Foot Clan. However, he became increasingly uncomfortable with Splinter's methods. And upon Splinter's execution of Darius Dun, Raphael changed his mind and decided that Michelangelo had been right all along, leaving the Foot Clan along with Donatello and Leonardo, and moving back into their old lair.
During the days that followed, Raphael participated in a raucous Christmas party, assisted Angel Bridge in bringing a traumatized Alopex back to New York, and infiltrated the Pantheon Family Reunion, with nearly-deadly results.
He returned to Dimension X with his brothers in The Trial of Krang story arc, in which they were required to bring back a collection of key witnesses to testify against Krang. During the trial, he participated in the defense of Planet Neutrino from the Malignoid swarm. Afterwards, he and his brothers were attacked by the Collectors, and Raphael was forced to go on an inter-dimensional journey with Ray Stantz, resulting in his body temporarily being stolen by Viking ghosts.
His strained relationship with Splinter became even more so when the Turtles returned to Earth, and found the Foot Clan in conflict with the Triceratons. When Splinter attempted to imprison the Turtles for their own safety, Raphael was particularly outraged. He later accompanied his brothers to attempt to defuse the situation, defeating the Elite Foot ninja in the process. When Burnow Island was attacked by Bishop, Raphael was reluctant to assist the Utroms and Triceratons, but accompanied his brothers anyway.
He was captured by Agent Bishop shortly afterwards and experimented on, as the E.P.F. wished to know what made the Turtles different from other mutants. They intended to kill and dissect him, but Raphael broke free and escaped, reminded of Buck and his own losses and pain from the past. He defeated many E.P.F. personnel, before being rescued by Casey, Angel and Alopex.
Unlike his brothers, a great deal of Raphael's personality was shaped by his early life on the streets. He tends to speak in a rougher manner, wishes to intervene if he sees an unjust fight, does not hesitate to use his fists, and experiences feelings of loneliness that his brothers do not feel.
He also has a very volatile temper, which he inherited from his father. Raphael tends to act impulsively and violently because of this, unless checked by his father or one of his brothers, and often fights verbally or physically to cope with feelings of guilt or insecurity.
Of particular note is Raphael's sensitivity to the idea of losing family members. Having experienced isolation his brothers have not, he reacts strongly to the idea of losing one of them, such as in The War to Come, when he confessed to fear that one of them would not survive their breakneck adventures. When Leonardo was brainwashed by the Foot, his loss weighed heavily on Raphael. He was similarly devastated when Donatello was nearly murdered by Rocksteady and Bebop, and showed lasting concern for his brother's well-being long after Donatello recovered.
In the course of his adventures with his family he also built a close relationship with the mutant fox Alopex, especially because the two are perhaps too similar in temperament and life situation. Their friendship is perceived as potentially romantic by some friends and family, though Raph has ruled out the possibility of the two of them being mates for basic biological reasons.
- It is revealed in issue #5 that Raph's favorite color is red.
- As seen in his bedroom in issue #65, he is a fan of the Marvel character Wolverine.
- It is revealed in "Micro-series: Raphael", that Raph goes on patrol in the city with Casey on Wednesday nights. According to the Annual 2012 issue, he says that it keeps them sane.
- He practices tai chi.
- He is right-handed.
- He is mildly claustrophobic, as revealed in the Leatherhead arc.
- He secretly wants to be a farmer.
- He is the first of the Turtles shown to remember his life as an ordinary unmutated turtle.
- He is the third of the Turtles shown to remember his human life, specifically of being an unborn baby.