Some of the dialogue in this chapter is from the comics, issue #11 and #12 to be exact, so I can't take credit for all of it.

Raphael stiffened as the Foot ninja in the building rose almost as one, their blades in their hands, rising like silver blades of grass around the rat. The only one who wasn't was Karai, who had raised her bow and was aiming an arrow straight at the rat's head.

Hamato Yoshi's head.

Who was Hamato Yoshi? Raphael found himself wondering, perplexed. Master Shredder spoke as if they had known each other a long time, but he hadn't recognized the rat until he spoke. In fact, he seemed puzzled by the fact that Hamato Yoshi was a rat at all… had this rat once been a human, and somehow transformed into a rat? That wasn't possible, was it? All Raphael knew of the mutagen was that it transformed animals into mutants like himself, but he didn't know what the effects were on humans…

Once again he was sorely tempted to step out and ask questions. But, he reluctantly told himself, they would have to go unanswered, because Master Shredder had ordered that the rat was to die. If Karai didn't kill him successfully, then Hamato Yoshi would fall before the dozens of Foot ninja present…

Karai's arrow sang through the air, but the rat simply slashed it out of the air with his katana, cleaving it in two. Raphael's eyes widened — that was a feat that only a few people he had seen were skilled enough to do. One of them was Master Shredder.

"Useless girl," Shredder growled, now masked and helmeted again. "Foot ninja, attack!"

They obeyed, dozens of dark-clad figures leaping towards Hamato Yoshi with weapons at the ready — katana, tanto, bo, nunchaku, anything else that could fell a single rat mutant with a sword. Raphael expected the rat to tire and give out quickly, but to his surprise Hamato Yoshi didn't seem to be losing his energy — he spun and leaped, kicking ninja in the face and slashing them with his katana. They fell like flowers cut by a blade, crumpling to the ground until none of them were left standing.

"Now…" Hamato Yoshi said grimly, facing Master Shredder, "shall we continue?"

Master Shredder turned slightly towards Raphael, and his dark eyes glinted under his helmet. "Raphael… you may join the battle."

"Yes, Master," Raphael said immediately, stepping out of the shadows and warily approaching the rat. His hands pulled his sai from his belt, twirling them briefly before clenching them between his fingers. Normally he wouldn't have been so cautious, even of a mutant, but after seeing him defeat so many foes at once… well, there was no shame in being careful.

But he wasn't prepared for the rat's reaction. Hamato Yoshi stared at him with wide eyes, slowly taking in the turtle's appearance from his toes to the black mask across his face. Every inch of exposed green skin, every fold of black cloth, every detail of Raphael's face. It made the turtle feel vaguely uncomfortable — he was used to scrutiny and being stared at, but the rat stared at him as if he truly could not believe what he was seeing.

"Raphael?" Hamato Yoshi whispered at last. "Is it really you?"

Raphael blinked. "I don't know you," he said.

Sadness crept into the old rat's eyes, as if Raphael's words had pierced him to the heart. "No," he said softly. "You do not. Not now."

"Kill him, Raphael," Master Shredder said, his voice dripping with hate.

Raphael dropped into a stance, his sai in his hand ready to catch and snap the blade of the rat's katana. He didn't particularly want to do this — he had too many questions that needed answering — but he knew that refusing would only lead to his own death as well as Hamato Yoshi's. He remembered the savage beating he had suffered all too well, and he knew that there would be no such mercy this time around.

"I will not harm you, Raphael," Hamato Yoshi said quietly, raising his sword. "Never will I harm you. But neither can I allow you to harm me."

"Why are you acting like you know me?" Raphael said, feeling irritation rising inside him. "I've never seen you before!"

"Not for a long time," Yoshi corrected him gently. "But not never."

"What the hell does that mean?" Raphael snarled. He lunged towards the rat without waiting for an answer, acutely aware of Master Shredder's gaze on the back of his neck, and swiped outwards with his sai.

But Yoshi dodged his blows with seemingly little effort, his eyes still fixed on Raphael's face as he bent and swayed aside. Raphael could feel his anger boiling as he lashed out again, only for his blows to be either avoided or easily turned aside. Yoshi's sword swept down and wrested one of the sai from Raphael's hands, fast enough that the turtle was unable to deflect the blow, sending it spinning up into the air before embedding itself in the floor.

Clutching his remaining sai, Raphael crouched in a more defensive pose, trying to find a chink in the rat's armor. How could he be this good? he thought incredulously, watching the rat shifting into stances he didn't even recognize.

"I do not wish to fight you, Raphael," Yoshi said quietly. "Put down your weapons, and we can leave this place peacefully."

"What makes you think I want that?" Raphael snapped.

He flung himself forwards with a roar, the point of his sai aimed towards Yoshi's throat. Why did the rat keep speaking as if he knew him? For some reason that angered him — it was as if Yoshi didn't recognize that he was part of the Foot Clan. Wouldn't acknowledge him as part of it. He knew what his life had been up to this point — the Foot Clan, for as long as he could remember. Now Yoshi was trying to confuse him, acting as though it was something he could just leave behind…

He didn't see the sword swinging up until it struck the sai from his hand, and then swept down towards his neck. The thought But he said he wouldn't harm me! flashed through Raphael's mind as he saw it coming… only to be sent stumbling back, unharmed except for a stinging welt on his shoulder. Yoshi had struck him with the flat of the blade, not the edge.

Before he could recover his feet, he felt clawed fingers closing on his throat — and the world around him began to waver and darken as if the rat had flipped a switch. Raphael gasped and clutched at Yoshi's arm as his legs turned to jelly and collapsed under him.

"I am sorry, my son," Yoshi said quietly. "This is the only way I can keep you out of harm's way."

"What — did you —" Raphael gasped.

His body went numb, except for some tingling along his arms and legs, and he collapsed to the floor. He wanted to scrabble back to his feet, wanted to rejoin the battle for his master's sake. But the darkness encroached on him from every direction, until he could barely hear Yoshi's voice echoing through the empty building.

"You murdered my beloved Tang Shen, Saki, and ruthlessly executed my precious sons before my very own eyes," Yoshi was snarling. "Then you took my life without allowing me the warrior's honor and justice only the purest combat can provide."

Took his life? Raphael's fogged brain struggled to understand what he was hearing. Yoshi had somehow been dead… and come back as a rat mutant? None of this made any sense…

"And yet, here I stand in this next life, prepared to make good on my final promise to you in the last."

Master Shredder's voice took on the edge of a sneer. "So, Hamato Yoshi, removing your head was not enough to cleanse your traitor's stain from this world, hm? Instead, you return from the dead a monstrosity that dares call itself master." He cast aside his scarlet cape, his eyes gleaming under his shining helm. "You may have been a master once, Yoshi, it's true. But even then, you were my inferior. In the end, just as you have admitted here, you failed to protect your wife, your sons... yourself."

He raised his bladed gauntlets. "And, now? Now you are nothing more than a rat in a trap."

Raphael fought past the darkness, pushed his fists against the concrete floor and tried to will himself upright. Strange tingling sensations were shooting through his limbs, and his head was swimming as he tried to raise it a little too fast. He could hear blades clashing — Master Shredder's voice speaking of Yoshi's impending defeat —

Finally he managed to struggle to his feet, and mechanically picked up the fallen sai from where Yoshi had thrown them. His vision was finally clearing of the dark mists that had rolled in over his head, and he could feel his extremities normally again. He stood up straighter, watched as Master Shredder loomed over the collapsed Yoshi, his blades glinting in the faint light.

"My sons," Yoshi murmured. "Forgive me…"

And for a single second, his eyes turned to Raphael, with that same sad expression, as if he were mourning something forever lost.

Then something crashed through one of the windows overhead, scattering shattered glass before landing on Master Shredder with a loud thump. He staggered to the side, dazed by the unexpected intrusion.

"You mess with our father," a voice rang out, "and you mess with us!"

Four shapes were leaping down from the broken window. One was a human, his face hidden by a hockey mask. The other three were green-skinned except for their golden-tan plastrons, their backs covered with hard curved shells, their faces masked in scarlet, and their hands clutching ninja weapons that Raphael recognized almost as well as his own sai.

He watched in stupefied amazement as three other ninja turtles leaped into the room.