Family and Allies
Tang Shen: Both Hamato Yoshi and Oroku Saki loved Tang Shen very much, but her decision to marry Hamato drove Oroku into learning about his place in the Foot Clan and turn against his adoptive brother one night, when he broke into the Hamato Clan monastery and attempted to kill Hamato in a duel. However one such blow meant for Hamato struck Shen instead, by accident and burned the monastery down. Naturally, Hamato was absolutely devastated when Shen died.
Hamato Miwa / Karai: Karai is none other than Splinter's biological daughter. In the episode Showdown Part 2, Splinter discovers this after the Shredder reveals to him that he took his daughter, Miwa, away and raised her as his very own child. When Karai soon shows up, he is then able to turn Splinter's own daughter against him by using what he had formerly told her about whom killed her mother, Tang Shen. She then tries to fight Yoshi, but her manages to avoid her attacks and escapes. She then demands to know why he won't fight with her and calls him a coward. He then leaves, heartbroken at what the Shredder has done to his daughter. In Follow The Leader, she demonstrates how truly spiteful and vengeful she has now become towards him. She hates him to the point where she wanted to kill the Turtles before his very eyes and ruin his life in so many more ways. When she successfully tranquilizes Splinter in The Manhattan Project, Part 1, she seems to view this as a big victory and she also even appears to draw some sadistic pleasure from doing this.It is very clear that Splinter knows that his daughter is fully alive, active, and working alongside the Shredder, In The Manhattan Project, part 2, she over hears splinter talking to the team about him being her biological father and whether if she will figure it out and accept it is her decision. She then has a guilty expression on her face suggesting that she's starting to question herself and everything else. In The Wrath of Tiger Claw her knowledge of the truth caused all her hatred of him to disappear and after her rescue in Vengeance is mine she hugged him for the first time. After her mutation into a snake-like creature, her love for him gave herself the strength to fight her new instincts and not devour him. When Splinter was seen drowning at the ending of The Invasion, Part 2, she quickly swims towards her father to save him. Before leaving, she touches him with her nose to his face.
Leonardo: Leo loves to train, spar, and learn more about ninjutsu. He likes to train with his sensei, and father; Master Splinter. Splinter taught him everything he knows about ninjutsu, and Leo respects him very much. Out of all the turtles, Leo has the closest relationship with his father, very often going to him for advice. Like his brothers, Leo is very protective of his father as well. Leo was the first turtle to call Splinter "father" in a long time.
Raphael: Raph loves Master Splinter as a father and a sensei. He often tries to prove to him that he's better than Leo. Splinter is aware of Raph's temper and often must give him a guiding hand to keep his anger in check. Splinter can be hard on Raph, especially when he picks on his brothers, but never the less sees great potential in him. Splinter often wishes Raph would think more before reacting when it comes to battle. Like with all his sons, Splinter is very protective of Raph. Raphael loves his father, and showed much concern when he was taken over by the Rat King in I, Monster. Raphael even gave Splinter a hug when Splinter came back to his senses. And in The Invasion, Raph really lost temper for seeing Shredder throw Splinter to the flowing sewers and he can't do nothing.
Donatello: Donnie loves Master Splinter, as his father, but he sometimes questions his wisdom as seen in Monkey Brains. Splinter praises Donnie for his intelligence and skills as a ninja, but wishes for him to think a little less in battle. He even hugged his father when he came to his senses as seen in I, Monster. Like with the others, Master Splinter is very protective of Donnie.
Michelangelo: Michelangelo is loyal and obeys Master Splinter's rules. However, Master Splinter is also highly aware of Mikey's lack of maturity. When Splinter was asked if he had ever considered naming Mikey the leader of the team he replied, "No. That would have been....wrong." But he still loves Mikey, as much as he does with the rest of his brothers. Splinter even acknowledges Mikey's wise choices, such as when Mikey rescued Leatherhead from the Kraang, or when Mikey (Accidentally, considering there was no one else to blame) said that Splinter shouldn't have allowed them to go to the surface, because he taught the turtles to fight as individuals, not as a team. Mikey even gave Splinter a hug when he came back to his senses in I, Monster.
April O'Neil: Splinter views April with fatherly fondness and as implied in Panic In The Sewers, has been training her to be a kunoichi (or female ninja); also noticing her innate sensitivity to her surroundings.
Casey Jones: Despite Casey's fear of rats, Splinter is patient with him and even calls him "My friend" when he tells the human teen that he doesn't have to fear him and that he "does not bite". In The Wrath of Tiger Claw, Splinter helps April look after Casey when he is injured by Tiger Claw.
Spike / Slash: Splinter and Spike don't really interact much but before his mutation, Splinter asked him if he wanted to here a story after Raph's refusal. After his mutation he and Splinter appear to be on good terms at least until Clash of the Mutanimals, when the mutant tortoise struck him with his mace and abducted Raph. Slash later apologize for his forced actions, but Splinter knowing that Shredder was behind the whole thing says there was no need.
Leatherhead: At first sight, Splinter fought Leatherhead and easily defeated him for almost killing his sons. In The Invasion, Leatherhead rescues Splinter from almost being captured by the Kraang. Later, Leatherhead fought on Splinter's side against the Shredder and knocked him with powerful bites down and threw him against a wall. Shredder, who seemed to be deafeated, attacked Leatherhead from behind and was able to threw the surprised Leatherhead off the building.
Dr Tyler Rockwell: Splinter and Rockwell don't interact very often, but the former neurochemist seems ashamed of attacking Splinter while under Shredder's control, but Splinter easily forgave him knowing it was Shredder's doing.
Ice Cream Kitty: Despite being shown to be afraid of cats, Splinter seems comfortable with being around Ice Cream Kitty, due to her being the family pet she is shown to like him, even giving him a cheesicle when he seeks one
Other good Mutants
Oroku Saki / Shredder: Hamato and Oroku were raised in Japan as adoptive brothers and very good friends, and the two learned, exercised and became Masters in the art of Ninjitsu. However, their companionship suffered a great strain when they both fell in love with the very same woman, Tang Shen. They constantly competed for her attention, but she chose Hamato in the very end. Jealous, Oroku began harassing Hamato, insulting him and purposely trying to get him angry. This eventually culminated when Oroku learned of his true heritage and restored his birth clan as "the Shredder". Breaking into Hamato's own house and challenging him to a mortal duel, both men engaged in battle, and the house soon caught fire in the process (due to the fact that some burning candles were left laying around at the time), killing Tang Shen and horridly burning the Shredder's face. The latter found Miwa and secretly took her in, raising her as his own daughter and telling her many lies about what Hamato "did". Sixteen years later, the Shredder discovers that Splinter is hiding out in New York City, and he leaves Japan (along with his deployed Foot Ninja) to finish him off. The two finally meet again in Showdown, Part 2 and duel with each other in The Foot Headquarters. The Shredder soon reveals to Splinter that his daughter is indeed alive, and he attempts to have her kill Splinter when she shows up. With this revelation, it is likely that Splinter despises The Shredder even more than he formerly did. In Wormquake, the two were excepted to a duel in Shredder's Hideout when Splinter was recaptured, only to be rescued by the Turtles.
Tiger Claw: When Splinter and Tiger Claw saw each other, Splinter could've sworn that he knew Tiger Claw from somewhere.
other evil Mutants