This part is going to need some explanations. In the IDW continuity, Raphael and his brothers are the reincarnations of four teenage boys who were taught to use ninja weapons by their father, who was reincarnated as Splinter. So Raph's affinity for the sai here is not just because it's the signature weapon for the character, it's literally him subconsciously remembering that this was his preferred weapon.

Also, this is the only incarnation of the Turtles where they have a mother, Tang Shen. She's dead but did not reincarnate, instead appearing as a spirit to her sons when they are in need of her, such as when Leo is brainwashed by the Foot or Donnie is badly wounded and nearly dies.

"Do you know what these are, Raphael?"

Raphael looked around the spacious, dimly-lit room, at the gleaming blades and chains that hung from the polished wooden walls. He could see them extending down the walls, from the floor to the ceiling, like the severed fangs of a dragon.

"Weapons," he said hesitantly, wondering if this was a trick question.

"Precisely. These are the weapons that the Foot Clan has trained in for centuries, and we have raised them to nearly an art form," Saki said, raising a hand and sweeping it at the weapons on the walls. "You may choose a weapon for your own use. Any weapon in this room. Choose wisely."

A ripple of some indefinable emotion passed through Raphael, a shiver that made him feel vaguely fearful but also hopeful. Slowly he turned towards the wall, surveying the katana that was sheathed on a pair of display hooks. His hands brushed the sword, but then drew back. No, he thought, this wasn't right. Not for him.

He glanced over a pair of tonfa before moving on to nunchaku, a weapon that had frustrated him in the past. A kusarigama, with its wickedly gleaming sickle and long heavy chain. The ninjato, another sword. A kusari-fundo, which he didn't like the feel of — he preferred an object that was solid in his hands to one whose whirling and movements had to be controlled. A naginata… no, too long and difficult to carry, especially for someone his height. The bo staff was a little smaller, but it didn't feel right either. He wanted something with a blade or point.

He could feel Master Shredder and Toshiro-sensei's eyes fixed on him as he moved around the room, examining each weapon carefully. Sometimes he took the weapon down from its display hooks, and hefted it in his hands before carefully putting it back. None of them felt right.

Then a gleam of steel caught his eye — two long, pointed weapons with shorter, curving prongs on the sides, crossed over each other. Sai. Raphael carefully took them from the wall, and felt them slip easily into the palms of his hands, as if he were already familiar with them. His fingers closed around the slender steel, so that they protruded like claws from his hands.

A shiver ran through his body. These felt right. He felt… complete holding them.

"These," he said quietly. "I want these."

"Twin sai," Toshiro-sensei said meditatively, coming closer. "A good choice for you, Raphael."

Master Shredder made a satisfied sound in his throat, as if he had been planning for Raphael to take those weapons all along.

"We will of course continue practicing with other weapons, too," Toshiro-sensei continued. "But those will be yours, Raphael. And you will learn how to use them to the best of your ability."

"And then — he will fight well with them for the Foot," Shredder said, turning and leaving the room.

A strange look came over Toshiro-sensei's face, almost as if he were pained by the remark that Master Shredder had made. Raphael almost asked him what was wrong, but the expression was so fleeting that he almost thought he had imagined it.

That night, Raphael sat alone in his dimly-lit room, which was furnished with little aside from a futon, a low wooden table and a paper lamp. He had left his only real personal mark on the room by laying out the standard smaller weapons that he had been given, shuriken and kunai, which he had arranged in rows on the table.

But this evening his eyes were fixed on the sai. He couldn't seem to get enough of looking at them, turning them over in his hands and testing different grips and positions. He even tested the unusually sharp tips on his fingers, accidentally drawing blood from one of his thumbs as he did so. He stuck the thumb in his mouth absent-mindedly as he turned the sai in his other hand, holding it up to the light to see it gleam.

His practice the next day had been postponed, in favor of preparing for a mission he had been ordered to attend with Karai. It was a simple mission — they were meeting with representatives of the Mafia in order to secure tributes for the Foot Clan — but Raphael was not looking forward to it. He knew Karai hated him, and had hated him for as long as he could remember — although he was a little fuzzy on exactly why. Following her on a mission was not something he expected to enjoy.

He just had to endure it. If he could get through tomorrow, then it would be back to training with Toshiro-sensei.

With a sigh, he placed the sai on the table beside his shuriken, and scrambled over to his bed. It sometimes felt like the only place in the Foot where he could truly relax — the rest of the time, he was constantly tensed for training, for the dislike of the other ninja, for the desire to please Master Shredder.

The sound of voices caught his ear, and he raised his head to listen. After a moment he recognized them as the voices of his guards, two Foot ninja who stood outside his room all night, every night. Raphael wasn't entirely sure why he had guards — after all, even if he wanted to sneak out somewhere, there was nowhere else for a mutant like him to go.

On some nights, he left the door open and conversed with the guards before falling asleep. But on this particular night, he just wanted to fall asleep quickly, so the events of the next day would be over that much faster.

He pulled a coverlet over himself, rested his head on his curled arm, and closed his eyes.

He didn't actually remember falling asleep, only that the smell of flowers and fresh spring grass seemed to fill the room as he dozed, scents that he rarely ever encountered. Eyes still closed, he stretched out slightly and sniffed the air, a faint smile crossing his face.

"Do you like this place?"

He sat up sharply, looking around himself at the garden that seemed to have sprung out of nowhere. Maple leaves ruffled softly in the breeze, and willows dipped down over a babbling creek that fed into a small, peaceful pond in which a few large koi swam. Flowers seemed to rise from every spot that was uncovered by something else, curling out into the air and creeping into the path that wound through them.

And in the middle of it all was a woman, with long dark hair and an ornate kimono decorated with embroidered phoenixes. Raphael stared at her with mild perturbation, unsure what to say or do. She was beautiful — and better than that, there was a kindness, a softness to her face that was always missing from Karai's, or those of any of the other women he had encountered in the Foot.

She seemed vaguely familiar to him, as if she were a person he had met once but forgotten over time. And yet, this woman didn't seem like the sort of person who would be easily forgotten.

Raphael scrambled up to his knees, looking at the woman. "I — yes, I do," he said hesitantly.

The woman smiled gently, and held out her hand to touch Raphael's face. He remained still and silent as she caressed his cheek.

"That is good. I hoped that this garden would bring you some peace of mind."

He blinked up at her. "Who — are you?" he said.

She leaned forward and pressed her lips between his eyes. "Does my brave son not know his own mother?" she said gently.