Raphael is the strongest and toughest among his brothers, being able to take on much larger opponents quicker and more easily. If used correctly, his temper can boost his strength and increase his fighting prowess. Like his brothers, Raphael is stealthy, can hide in the shadows, sneak around without being detected, and use hand-to-hand combat, Taijutsu. His exceptional skills in battle may be partially due to the fact that he does not mind risking himself in a fight (this is also shown by his appearance - his mask is very tattered and worn, and he has several chips and scratches on his shell and body). His selflessness is most likely due to the fact that he may have a slight inferiority complex, and his fierce protectiveness of his brothers means he will put himself in a line of fire to protect them.
Raphael is also seen to be quite intelligent when he thinks clearly, and often takes the role of second-in-command. He has also demonstrated the ability to take control of, or influence animals (mainly pigeons) to help out. The extent of this ability has not yet been fully explored and it is unknown whether or not it will be shown again. It is also shown in Slash and Destroy that Raphael is able to use the famous Pressure Point technique which he uses to defeat Slash.
As far as Raphael's flaws go, the biggest, and most obvious, is his temper. He starts to deal with his anger issues in Turtle Temper, after being told by Master Splinter that anger can be very destructive (via a story that explained why the Shredder killed Tang Shen). Throughout the rest of the series, he is slightly less impulsive; however he is still the most aggressive of his brothers, and always becomes extremely angry when one or more of his brothers are hurt. He is less vicious to his brothers after this, but still hits them when they are being annoying.
While down in the sewers, Raphael beat Donatello and then he fought Leonardo, (who beat Michelangelo in a fight before) and then won the training tournament by throwing Leonardo with his Sai. However, when Splinter congratulated them, Raphael bragged about his win, which caused Splinter to hit a pressure point on his neck and forced him to compliment his brothers. The Turtles are later seen eating a dish Michelangelo prepared called "Algae and Worms." After the meal, Splinter relays the story of how they were transformed (which is fairly different from the other origin stories told in the other series).
Fifteen years before the Rise of the Turtles, Part 1, the benevolent Hamato Yoshi purchased the four turtles. Yoshi came into contact with a rat and had to fight against a couple of Kraang. The aliens dropped theirmutagen, causing the mutation of Yoshi and the Turtles. Yoshi raised the Turtles as his own children and continues to train them in ninjutsu. Splinter agrees after some begging to let the Turtles go to the surface. It is here that Raphael scares a Pizza delivery guy who speeds away on his motorcycle. The four of them, curious, open the box, and, after Michelangelo tries it, eat (and very much enjoy) the pizza.
Always acting before he thinks things through, Raphael is the muscle of the team. He is catty, sarcastic, tough, and at times, mean; but he is known to have a soft side when caring for his pet turtle. It is also shown that he loves his brothers very much, and shows his nurturing side at times, mostly to his younger brother Michelangelo. However, he often feels that his family doesn't understand him so he doesn't usually open up to them.
As seen in New Girl in Town, Leonardo and Raphael begin to argue. When this happens, Leonardo decides that Raphael should lead the team, if he can do better, to which Raphael agrees. During this, they battled Snakeweed, and Michelangelo ended up injured. Raphael said he 'froze up seeing Michelangelo like that'. He told Splinter he needs Leonardo. He also said, "I don't mind risking my own life, but risking my brothers'..." This shows us how much he cares about his brothers.
As far as humour goes, Raphael (like most of his incarnations) is very cynical and sarcastic, sometimes making jokes at the others' expense, but usually just making 'witty remarks'. He also deadpans a lot—for example, when Donatello sees April for the first time, and says "she's the most beautiful girl I've ever seen" Raphael then asks "isn't she the only girl you've ever seen?" Humour is generally when he is most amiable to his brothers too. For example; he will tease one, and another will usually agree or join in—these jokes are often at Michelangelo's expense, (but he rarely minds) or at Donatello's if April is mentioned (occasionally, Raphael and Michelangelo make kissing noises when Donatello mentions her).
As far as Raphael's flaws go, the biggest, and most obvious would be his temper. He starts to deal with his anger issues in Turtle Temper, after being told by Master Splinter that anger can be very destructive (via a story that explained why the Shredder killed Tang Shen). Throughout the rest of the series, he is slightly less impulsive; however he is still the most aggressive of his brothers, and always becomes extremely angry when one or more of his brothers are hurt. Raphael is less vicious to his brothers after this, but still hits them when they are being annoying.
During most of the series, Raphael wields twin Sai, with which, like his brothers and their chosen weapons, he is highly skilled. In Pulverizer Returns, Master Splinter says that the boys are relying too heavily on their own weapons and makes them swap. After this process, Raphael is left with Michelangelo's Nunchucks. His Sai are given to Donatello. Despite their best efforts, none of them are particularly successful (mostly Donatello, who manages to prick himself with the Sai) however, Raphael only hits himself twice with the nunchucks, meaning he is at least somewhat competent with them (mostly likely because they are of a similar design, ie: two, small handheld weapons).
However, during a more difficult fight, the turtles are still uncooperative with their new weapons and swap back. When Splinter finds out, he confiscates all weapons, stating that anything can be useful. When he and his brothers are trying to save Timothy, Raphael uses two planks of wood, holding and fighting with them in a style similar to his Sai. In The Gauntlet, he used a Yumi bow and like his other brothers wields Shuriken (throwing stars). In Booyaka-Showdown, Part 1, Raphael armed himself with Kama scythes, Shuriken, Kunai, Tonfa and Brass Knuckles.
- In New Friend, Old Enemy When it shows a close up of Leo and Raph, right before they charge at the Foot soldiers, Leo has 4 swords. 2 in his hands and 2 in the holder on his back.
Raphael's plot in the episode Within the Woods is similar to the Mirage volume 1 story arc Down to the River, River Hymn And Old Man River, where Raphael had some of his mutagen sucked out of him by a river leech (later named Bloodsucker), which caused the leech to mutate and Raph's mutation to become undone. Bloodsucker succeeded in finding Raph and sucking out the rest of his mutagen, changing Raph into an ordinary turtle and Bloodsucker into a sentient creature. Eventually, the creature's mutagen is transferred back into Raph, who changes back to normal. The primary differences between that story and this episode are:
- The creature, Creep, is river scum, not a leech like Bloodsucker. Creep was initially mutated by the mutagen-based medicine Donatello gave to Leonardo to help him heal. The medicine nauseated Leo and he vomited it onto the river bank and dropped the rest of the bottle. Bloodsucker's initial mutation was caused by drinking from Raph directly.
- When Raph had his mutagen sucked out of him, he turned into a plant, not an ordinary turtle.
- Donnie transferred the mutagen from the captive Creep back into plant-Raph to turn him back into normal. In the Mirage story, unmutated turtle Raph sucked the mutagen out of Bloodsucker directly to change both of them back to normal.