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One night while heading home from work, news reporter April O'Neil is attacked by a band of juveniles working for The Foot. Raphael threw a ski to destroy the nearest street light, allowing the Turtles to easily defeat the criminals. However, he was unable to retrieve the sat before the police arrived and April claimed the weapon.
The loss of his weapon troubled and angered Raphael, who was determined to reclaim it despite Splinter's orders. He left to watch a movie aboveground, and on his way home encountered two purse-snatchers, whom he frightened into running off. However, upon pursuing them, he encountered the vigilante Casey Jones and prevented Jones from injuring the criminals. Jones responded by knocking Raphael into a trash can and referring to him as a "freak," which enraged Raphael further.
Upon returning home, Raphael found Splinter waiting for him, in order to speak to him about his anger. He appealed to Raphael to not forget his brothers or father as he fought his rage.
Still unwilling to abandon his lost sai, Raphael trailed April O'Neil from the police station to the subway, where she was attacked by a squad of Foot ninja. When she was knocked unconscious, Raphael retrieved his sai, attacked the ninja and escaped into a train tunnel. Unbeknownst to him, one of the ninjas followed him back to the lair.
After Splinter told April of their origins, the four Turtles accompanied April back to her apartment, and Raphael spent most of the evening in her company. However, when they returned home, they found the lair ransacked and Splinter missing. Raphael was overcome with grief and rage.
He remained troubled and angry as they waited for April to discover new leads on the Foot ninja. He argued with Leonardo, insisting that they should find Splinter rather than waiting, before leaving for the rooftop.
However, he was ambushed by a large number of Foot ninja, who savagely beat him before throwing him through a skylight. Unconscious and nearly dead, he was carried by his brothers to a van parked outside, and transported to April's remote farmhouse.
Still comatose, Raphael was placed in a bathtub upstairs, and a guilt-ridden Leonardo stood vigil over him. When Raphael finally awoke, Leonardo apologized to him, and the two brothers reconciled. In the days that followed, Raphael recovered completely from his injuries. However, he remained troubled by the loss of Splinter, and was deeply moved when they were able to psychically contact their lost father.
The Turtles chose to return to New York in order to save Splinter. On their first night back, they were attacked by the Foot Clan, much to Raphael's delight. When the Shredder appeared on the rooftop, Raphael was the first to attack him, but was easily knocked to the ground. When a defeated Leonardo was held at spearpoint by Shredder, Raphael was the first to throw his weapons aside in exchange for his brother's life.
Just as Shredder was about to kill Leonardo, Splinter reappeared and defeated Shredder, throwing him from the rooftop into a garbage truck. Overjoyed, Raphael embraced his father and remained attentive to him as his brothers celebrated their victory.
Along with his brothers and Splinter, Raphael temporarily moved into April's new apartment. His mood was noticeably improved now that the Shredder was seemingly dead, though he was beginning to chafe under the secrecy that they lived under, and there was still tension with Leonardo.
Upon learning that the ooze that mutated them came from TGRI, Raphael accompanied his brothers to the facility to investigate further. They encountered Tatsu and the Foot ninjas there, and began fighting for possession of the last canister of mutagen. This loss of the canister weighed on his mind as the Turtles prepared to leave, but he was temporarily distracted by the arrival of the pizza boy Keno, who had figured out that the Turtles were living in April's apartment.
When the Turtles went out in search of a new home, Raphael expressed his frustration that they weren't pursuing the Foot at present. This lead to another argument with Leonardo, and Raphael left moments before his brothers uncovered their new lair. He enlisted Keno to help him by pretending to be a new recruit for the Foot, but was ambushed and captured by Foot ninja before his plans could be carried out.
He was left bound and gagged in a junkyard as bait for his brothers, who came to rescue him but were nearly killed themselves. Once Donatello freed him, Raphael attempted to take down Rahzar but was unsuccessful, and the Turtles were forced to withdraw before the mutants had a chance to overwhelm them. Their next confrontation was somewhat more successful: he and Michelangelo were able to knock down Tokka and Rahzar long enough for Donatello to catalyze the anti-mutagen, reverting them back to a normal snapping turtle and wolf.
Just as the Turtles thought they had defeated Shredder, they discovered that he had instead been exposed to the mutagenic ooze, which transformed him into a "super-Shredder." Along with his brothers, Raphael escaped into the ocean and was able to swim to shore, leaving the Shredder to be crushed under a falling boardwalk.
Along with his brothers and Splinter, Raphael witnessed a magical scepter transport April through time and space to feudal Japan, leaving Kenshin in her place. He was willing to go back through time to rescue his friend, but the situation became substantially more complicated when the Turtles actually did so, as they were exchanged with four horse-mounted honor guards in the middle of a battle. With Michelangelo and the scepter missing, Raphael followed Leonardo to the nearby castle, which they barely managed to infiltrate without being found out, although Raphael's temper nearly got the better of him when he was confronted by Niles.
They managed to locate and free April, but were confronted by a host of guards who kept them from being able to leave except via a sewer drain. After going out in search of Michelangelo, the three Turtles encountered the rebellious villagers, whose village was under attack by the forces of Walker. After the ensuing battle, Raphael attempted to learn how to ride a horse with limited success. He also formed a bond with a young boy named Yoshi, advising him on his aggression and comforting him when he was frightened. It was due to his connection to Yoshi that he was able to briefly reclaim the lost scepter.
However, when it was taken by the mercenary Whit, Raphael accompanied his brothers into the castle to reclaim it and the rebel leader Mitsu. They took part in a massive battle between the daimyo's soldiers, Walker's men and the rebel villagers, which ended with the scepter being regained once again.
Raphael briefly considered staying in the past, recognizing that people did not appreciate or accept him in his own time as they did in feudal Japan. However, he was swayed into returning to the present, after saying goodbye to Yoshi.
At the start of the 2007, CGI sequel TMNT, a now 19 year old Raphael, growing increasingly frustrated and violent over Leonardo's absence, has become a masked vigilante, the Nightwatcher, going to the surface at night and fighting crime in a very brutal fashion. When Leonardo returns from Central America he confronts him in his Nightwatcher disguise, and toys with Raphael who, using the manriki, is not a match for Leonardo. Leonardo knocks off his helmet with an uppercut and then, seeing its Raphael, starts to lecture him. He and Leonardo then come to blows and, in a bout of focused rage, he breaks Leonardo's katanas and pins him to the ground, his sai striking an inch from his brother's head. Leonardo's staring causes him to snap out of it and retreat. After Leo is kidnapped by the stone Generals and Foot Clan, Raphael attempts to save him, but fails, and returns to the lair, distraught. Here, it's stated that some of his jealousy towards Leonardo is because he was the apparent favored son of Splinter; after Splinter assures him that he is just as valued as all his brothers, he effectively leads the Turtles (joined by Splinter, April and Casey) in a rescue, giving Leo a new pair of swords to replace the ones he destroyed in their fight, effectively passing the baton to his brother and accepting him as leader.
- The film version of Raphael makes brief appearances in Turtles Forever and All Tomorrow's Yesterdays.
- According to the T files on the DVD extras of the 1990 movie, Raphael's:
- Favorite color is red, (for many reasons, none of them good, all of them appropriate).
- Hobbies are hockey, baseball, golf (which are mostly things he does with Casey Jones.)
- Favorite music is rap, metal, punk, and "Grunge".
- Favorite foods are pizza and cereal.
- Favorite book is Jurassic Park by Michael Crichton, which he thinks is better than the movie.
- Is right-handed, although this is contradicted by his appearance in the TMNT 2007 movie where he is shown to be left-handed.
- Height is 5'
- Weight is 170 lbs.
- Eyes are brown.