Some dialogue in this is from Issue #12 of the comics.

For a moment, Raphael was too shocked to react to what he was seeing — other mutant turtles, so like him in appearance that he doubted that most humans could tell the difference. One of them, carrying a pair of sheathed katanas on his back, passed so closely that Raphael could have reached out and touched him.

"Kill the intruders!" Master Shredder bellowed. "Kill them all!"

The one with the swords leaped towards Karai with both his weapons out, while the ones with the nunchaku and bo launched themselves into the fray with the Foot ninja who had recovered from their beating. The human was swinging what looked like a baseball bat and a hockey stick, but seemed to be doing fairly well even against trained ninja.

Raphael gripped his sai tightly, and launched himself into the battle. He felt as though everything was spinning out of control — as if unknown forces were trying to peel him away from everything he knew. He was of the Foot Clan. There was nothing else for him…

Then a bo caught one of his sai, throwing him backwards, and a pair of dark brown eyes looked down at him, widened in disbelief.

"Raphael?" the turtle gasped.

Raphael sprang back to his feet, taking a few steps back from Bo. "How do you know my name?" he demanded.

"We've been looking all over for — unh!" Bo staggered backwards as Raphael's fist connected with his abdomen. Tears sprang to his eyes as he planted his feet firmly, and spun the staff in his hand. "Okay, I'm sensing you're not in the mood to talk."

"How do you know my name?" Raphael roared.

"Is that Raphael?" Nunchaku yelled out, leaping overhead with his weapons spinning.

"It sure is, and he doesn't seem happy to see us," Bo said grimly.

"Seriously? He's one of them?" Nunchaku said incredulously, sending two Foot ninja flying through the air. "How did that happen?"

Raphael crouched down, ready to spring towards them as soon as he figured out what move they were going to make. His head felt like it was splitting in half — on one hand, he knew that he had to eliminate these threats to the Master, these intruders who were getting into his mind, making him wonder things he shouldn't be wondering…

And on the other hand, he desperately wanted to know what they meant, what they knew about him that he seemingly didn't even know about himself. How could they have been searching for him all this time, if no one outside the Foot even had known he existed? How had they known his name when it was Master Shredder who had named him? And why did they call the rat their "father"?

The pain behind his eyes intensified, and he swallowed hard, his eyes fixed on the turtle in front of him. Every hard line of his stance was immovable, as sharp as a diamond embedded in steel, and his sai gleamed in the faint light as he raised them.

"Raphael, listen to me," Bo said urgently. "You shouldn't be doing this — you shouldn't be here at all. We've been looking for you for months — we want to bring you home with us!"

"Stay away from me!" Raph snarled.

"Guys, less talking and more getting Father out of here!" Swords shouted. He was standing over Karai's crumpled body, his swords still shining in the light, and Raphael found himself reflecting that he wouldn't be too upset if Swords had killed her.

"He won't listen to me!" Bo shouted.

"Shut up!" Raphael snarled. He lashed out with one of his sai, almost scraping the side of the other turtle's face, but thwarted by a last minute jerk of the head.

"Leave him, Donnie!" Swords shouted. But Raphael caught a glimpse of his face, and the twist of pain that clung to the other mutant's features, as if it had hurt him to say those words. "We can't rescue Father and Raphael at the same time! There are too many of them!"

Bo threw one more anguished look at Raphael, and backflipped away towards Yoshi. Raphael threw himself after Bo, trying to grab the mutant rat before the other turtle could, but found himself blocked by a pair of crossed katana blades.

"Raphael," Swords said grimly, planting himself in Raphael's path. "We need you to listen. I know you must be very confused right now—"

"I'm not confused!" Raphael raged, lashing out with his sai.

Swords deflected the blow almost without trying, his dark eyes stern and sad. "Deep down you must know this isn't right — that you don't belong here. You belong with us."

"Shut up!" Raphael bellowed, his voice almost rising to a scream.

He didn't expect Swords to punch him — his eyes were on the shining blades in the other turtle's hands, so when one of his fists flew up and struck Raphael in the jaw, it came as a surprise. It was no simple brawler's punch either; the shock rippled through his already-weakened body, bringing him to his hands and knees. A raw gasp came from his chest as he struggled to rise again, able to see nothing before him but a pair of green feet and legs.

"We'll continue this another time," Swords said quietly.

As he struggled to rise from the ground, Raphael could hear the three turtles attacking Master Shredder — he seemed to be holding his own against them, calling out, "Your father is beaten, fools. He has lost, as will you if you persist in this futile battle. Instead, join the Foot—join me—and know victory!"

And despite the frenzy burning in his blood, Raphael achingly wished that they would throw down their weapons and accept. It would take away his confusion if they would — let him speak to them, listen to them without jeopardizing everything he knew to be right…

Swords called out, "Guys, listen up! We gotta work as a team—it's our only chance. Together, just like Master trained us."

They launched into another frenzied battle of swipes, kicks and strikes with blades, the three mutant turtles fighting almost like a single unified foe in their grace and strength. Raphael couldn't help but admire their form as they drove Master Shredder back, their weapons lashing out with skill and precision that Raphael had rarely seen in the Foot — certainly more than the average ninja he had battled before could ever hope to achieve. They were stronger, faster, more agile.

Then a horrifying thought rolled through his mind — they were going to kill his Master if they could. But… but he couldn't take on all three of them.

But as he staggered to his feet, the three turtles suddenly pulled back and retreated out the open window, the half-conscious Hamato Yoshi in their grasp. He could feel their dark eyes flicking towards him, with expressions ranging from sadness to confusion.

For some reason, the fierce energy of the fight seemed to drain out of his muscles, and he sank slowly to the ground, his breath coming in short harsh gasps. His chest hurt, his head hurt, and his mind was whirling with confusion that seemed to be tearing away at the core of his being, like shrapnel being blown through his heart. What was happening? What had these strange turtles done to him?

"Yes, flee. You only delay the inevitable. This does not end here," Master Shredder's voice boomed after them. "I am unyielding. I am unstoppable." His voice lowered. "I am the Shredder."

A shuriken went flying through the air, and embedded itself in the wall beside Master Shredder's head. Raphael goggled in disbelief as he saw that Swords had done it — at that range, and with his skill, he couldn't have missed by accident. He had done it on purpose. But why?

"I am… unimpressed," Swords said dryly, before turning and racing from the building.

Raphael watched silently as they fled, until the purple shadows of night swallowed them up, leaving behind only the groaning bodies of the wounded ninja behind them. Karai was stirring, clutching at her head and moaning loudly as she tried to fight her way back to her feet. Raphael hadn't seen what Swords had done to her, but apparently he hadn't tried to kill her — or even wound her that badly. Dammit.

And Master Shredder stood silently in the midst of all the chaos, his eyes burning with blackened fire.