Miwa was quickly given over to April's custody once the police had Oroku Saki down for child abuse. Though he denied all evidence against him, Miwa firmly put him in place when she started screaming about him leaving her brothers to die in the orphanage all those years ago and accusing him of killing her mother. Donatello and Raphael had both held her back, much to everyone's surprise, as it was usually Raphael who lost his temper first. Leonardo and Michelangelo were making sure that no one got near their siblings while their brothers tried to calm Miwa down. Though they could not keep the man in jail, as his lawyers were too good and he was still considered a humanitarian by many, they did manage to place a restraining order on him. He was not to be within fifty feet of any of the Hamato family, or their caretakers.
Miwa hated it and knew that he would somehow fight it someway, just to prove he could. Donatello and Raphael had decided to take the opportunity to try and surprise the others with a trip to the sewers. It was almost summer now, and they hadn't gone since Miwa had been injured. Donatello stayed with her everyday while his siblings collected his and Miwa's homework and brought it to them. Even with being out of school for so long, Donatello was still top of the class and he was still ahead of the rest of his class. He tutored Miwa so that she wouldn't fail her classes from being out at the hospital all the time. When they came in to finish their finals with their siblings, the Hamato children all scored the highest in the school, thanks to Donatello's tutoring; even Michelangelo!
Donatello had suggested that they go to their sewer home to celebrate, and was rewarded with the eager nods of his siblings. While Raphael had been going there constantly to keep the place clean and check up on their father, unbeknownst to anyone but Donatello, the others had yet to go back since Miwa had been hurt. They had instead been meeting up at the hospital where Miwa was staying. Donatello had been sleeping in a chair next to her bed since the whole mess started, wanting to be there for her in case anything else happened. While the hospital at first was reluctant to let Donatello stay, he had proven himself useful for keeping her calm, and Dr. Stockman had recommended it.
Now Miwa was back at full health and they had passed their tests. They wanted some place they could relax at, and their sewer home was the perfect thing for them. Raphael and Donatello were chuckling as they thought about their siblings reactions to finding their father there in the safe place they had made.
Master Splinter was meditating in the dojo, waiting for Raphael's daily visit with news of his other children. He liked that his son came and interacted with him still though he was a rat. It gave him a sense of normality. He was slightly concerned when he heard multiple feet heading towards his location. His concern turned to somewhat relieved when he heard the laughter of children and the conversations about the day.
He noticed the conversation come to a stop when the footprints did. He kept his eyes closed, fearing the worst. He would not dare lay a hand against his children after what he had done. He had left them. True, it was because he had thought that it was better than having them be raised by a rat, but in the end, his precious daughter had been hurt, and Donatello had been bullied. This he blamed himself for.
He then heard another softer set of movement. When the movement was gone, he slowly opened his eyes and found himself surrounded by his children, all in meditative positions, and all smiling while meditating with him, just as they had done as young children. Splinter wiped a small tear from his eye before continuing with his meditation. His family was reunited, and they were safe. That was all that mattered to him.