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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 throws his sai at the streetlight to cut off the section's source of light. While in the shadows, Raphael and his brothers attack and defeat the delinquents, and they also tie them up just in time for police to round them up.
However, Raphael lost the sai he had thrown which he forgot on the ground. Luckily for him, April picked it up herself and put it in her bag. The Turtles then retreated into the sewers back to their home. There they notified Splinter of their first battle against the recent crime wave. After a short speech about the way of the ninja, Raphael admits he lost one of his sai, but refuses to let it go. Instead he wishes to get it back, although Splinter says otherwise. For a second, he got into a shoving fight with Donatello, until it was stopped by Splinter.
Splinter then suggests meditation, in which the Turtles begin to dance to some music instead, except for Raphael. He gets his disguise, which was a trench coat and a hat, and heads off to go to a movie. He goes to the theater and watches the film Critters which he didn't like too much. On his way home, he encounters two teenagers robbing an old lady of her purse. He trips them and returns the purse to the victim as he scares the teenagers into running off. He then follows them.
As he follows them into the park, he encounters another vigilante by the name of Casey Jones who has also been upset by the recent crime wave. The two get into a fight with Casey's weapons, which are actually accessories used in sports, and eventually Raphael is knocked back into a trash can. Jones runs off, and Raphael tries to pursue him but fails. He returns home angry, where he is met by Splinter again. He then receives another lecture.
The next day April appears on the news interviewing the chief of police regarding the recent crime wave. Figuring out the reporter's location from the interview, Raphael heads to the police station to wait for her hoping to retrieve his lost weapon. After she finishes with her interview, April heads into the subway station secretly followed by Raphael. April just misses her subway train, and she frustratedly decides to wait on the next one when a gang of Foot ninjas jump her. She attempts to defend herself with Raphael's sai, which she had been carrying in her purse, but is easily disarmed. The sai is sent flying and April is knocked unconscious. Raphael retrieves his sai from where it landed and is able to defeat April's attackers. Using a speeding subway car to cover his escape he carries her through the subway tunnel to his home. A Foot Ninja secretly follows Raphael and is able to discover the Turtle's hideout.
He receives negative feedback from his brothers and Splinter for bringing a human into their lair, but he is nodded at for saving her life. When April awakens, she is frightened by Splinter and the Turtles, but when she is finally calmed down, Splinter tells her of their past. The Turtles then walk April home, since it was getting late. They lead her through the sewers and eventually take her up the correct manhole. She then invites them all into her apartment for some pizza. Sadly, when they return home they find out that their lair was broken into and Splinter was missing.
Later on, during a broadcast on live television, April expresses her gratitude to Raphael for saving her. Raphael is somewhat embarrassed and teased by his brother Donatello, but soon their argument ceases when he tosses a sai between Donatello's legs. Raphael then tells Leonardo that he wants to go out there and find Splinter, instead of waiting for something to come to them. They argue and then Raphael leaves to the rooftops to blow off some steam.
While there, he is jumped by many of The Foot ninjas. Because of Danny Pennington, their location had once again been revealed. Raphael then holds his own against the many ninjas for a short while, before being defeated and pummeled. After taking many hits, he is rendered unconscious and thrown through the window into the antique shop below. He can do nothing as his brothers fight The Foot to protect April and his unconscious body.
Across the rooftops, Casey Jones had spotted Raphael being jumped, and so he went over to help. He arrived in the middle of the battle, and helped out the Turtles greatly. He managed to buy them enough time to get everyone out, including himself. Casey then drove April and the Turtles to April's abandoned old house in the countryside. The Turtles had suffered their first real defeat, and April had lost her apartment.
The Turtles tried to recover from their loss by relaxing and honing their skills in the farmlands. Raphael was still unconscious, and the Turtles had put him in a bathtub to stay hydrated. When he awoke, he was greeted by Leonardo who apologized for the way he'd acted before. Raphael and Leonardo reconciled and hugged, only giving Donatello an opportunity to make a joke. Finally, the Turtles were four again.
Later on, after the mist cleared, more Foot ninjas stormed in, and the battle continued. The turtles gained the upper hand and drove the Foot out of the sewers and into the streets. Eventually the battle led up through the fire escape of a building until they reached the rooftop. There they brawled with the last of the Foot ninjas and defeated them. Just when they thought victory was theirs, the Shredder came down and introduced himself to the Turtles.
After a few quick jokes from Michelangelo and Donatello, Raphael took his turn against Shredder. He charged him but was easily tripped and knocked to the ground. The other turtles then took their turns and also failed. They tired out and then regrouped to try and make a game plan. Leonardo then realized that the Shredder was the one who knew where Splinter was, and so the four turtles all charged Shredder, one by one. After Shredder had beaten all four turtles it was Raphael who asked Shredder "Where's Splinter?" Shredder upon realizing who they were asking for, reviled that he had ordered Splinter's death. This sent Leonardo into a rage and he charged Shredder head-on. When Leonardo was pinned down, Shredder ordered the other three turtles to throw their weapons aside in exchange for their brother's life. Though they were reluctant to do so, Raph was the first to toss them aside. Splinter later revealed himself just as Shredder was about to kill Leonardo. After Splinter defeated Shredder and avenged his beloved master Hamato Yoshi, the four ninja brothers ran to the adopted father's side with Raphael embracing him.
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.