NOTES:
This work is another AU for the IDW comics continuity, although you don't need to know much about it to follow this story, since it branches off before they've even really mutated, and I'll do my best to include all information you need to know; if anything confuses you, just tell me. The origin story of the comics is that the Turtles were lab animals who were stolen by Foot Clan ninjas along with a canister of mutagen, which was splashed all over them when the bag they were in was dropped.
In the comics, Raphael gets separated from his brothers and father for reasons that aren't really relevant here, and ends up homeless and wandering the streets.
This fanfic wonders what would have happened if the Foot ninja - who were nearby and might have seen him if they had looked around - had noticed the last lab animal and brought it back to their clan... and what would have happened when he mutated at last.
It was an ordinary night at the genetic engineering company StockGen. A young intern named April O'Neil was studying, accompanied only by a rat named Splinter and four tiny baby water turtles in their glass aquarium. She had a special fondness for the turtles, having named them after four Renaissance artists.
But that ordinary night had changed when two black-clad ninjas had entered the building.
April's presence was no great obstacle to the two men — all they had to do was kill her before she could raise the alarm. As one of them attempted to do so, slashing at her with his sword, his compatriot took specific canisters of chemicals and piled them into a bag. Then he turned his attention to the tiny turtles, placing all four of them in the bag as well.
But before they could slay the girl, the fire alarm was suddenly tripped, distracting the ninja and drawing security to the laboratory. April smashed one in the head with a beaker, and fled as two guards rushed in.
Now the two ninja were clambering onto the rooftop, their hearts hammering in their chests. The one holding the bag could feel the turtles fluttering their tiny flippers inside, and privately wished that the little beasts would hold still while he was climbing.
The cold night air blasted past them as they reached the rooftops, and began running with all the speed they could muster. Neither had noticed that a tiny dark shape — a seemingly ordinary rat — had followed them there.
"Come on," the first of the ninja called out. He was still slightly groggy from the impact of the beaker.
"I'm coming," the second ninja called, clutching the bag in one hand.
Suddenly the furry gray shape hurtled towards his face like a bullet, clawing and biting at his eye. Blood spattered across his face, and a shard of white-hot pain shot through his socket. As he flailed in agony, he lost his grip on the bag, which was sent spiraling into the filthy alley below.
"Vile rodent!" he bellowed, rippling the rat from his face.
He threw the rat with all his strength, down into the same alley that the bag had fallen into. His damaged eye was bleeding now, half-blinded and agonizingly painful. He clutched at his face, groaning through gritted teeth.
"What happened to the bag?" the other ninja called out.
"Eye — can't see—" he grunted.
"Where is the bag?"
With another groan, he pointed down into the alley below.
The other ninja's eyes widened, and he drew in a sharp breath. It was too dark to see what had happened to the bag below them, but he knew that the glass beakers inside weren't designed to survive a fall that high. Neither, in all probability, were the four tiny turtles.
"Damned rat!" the wounded ninja choked, blood seeping between his fingers.
His compatriot turned and scrambled down the side of the building, his heart hammering against his ribs. He could hear the yowling of an alley cat somewhere nearby, followed by hissing and screeching. His fingers dug into the spaces between the bricks, and he cast a frantic glance down at the alley. He could see the bag, open and empty.
Even worse, he could see a puddle of something glowing down below him — something green and viscous. Something that should have been inside a glass beaker.
"No," he whispered, trying to move even faster.
"Wait for me!" his injured partner groaned, swinging himself down on the fire escape. Even with an injured eye, a true ninja was skilled at stealth and speed.
The other ninja cast another glance back the way they had come, at the StockGen building. An earsplitting alarm was ringing out, louder than the initial fire alarm — meaning that someone had alerted the authorities. As he raised his head, he heard the whine of a distant police siren — no several police sirens, ringing out in disharmony.
He scrambled the rest of the way down the building side, and his heart dropped. The beakers had indeed been broken, leaving a filthy green pool of liquid spattered with shards of glass. The ninja didn't know for sure what had been in those beakers, but he knew that it was sure to be a complete loss after spilling onto the muck-encrusted cement.
He landed on the ground with katanas already drawn, ready to fight if anyone entered the alley.
"Grab the bag!" the other ninja shouted behind him.
His eyes flicked over to where the bag lay on the ground. The rat was… the rat looked as though it was dragging the baby turtles into it. That wasn't possible, was it? It was only a stupid animal — how did it know how to carry off all the turtles at once?
"The rat!" his compatriot shouted.
With a desperate surge of energy, the rat pulled the bag violently towards the nearest storm drain. The ninja swung his sword with all of his strength, but missed by a single vital inch — it smashed into the top of the drain rather than the rat just below it.
"Damn!" he roared, flinging himself onto his stomach in a futile attempt to catch the bag before the damned rodent could pull it down into the sewers. But he was too late — just a few inches from his fingertips, he saw the turtles tumbling headlong into the darkness, with the rat falling ahead of them.
A silence settled over the alley, broken only by the distant sound of sirens.
The ninja huddled over the storm drain, suddenly feeling sick. They had failed in their mission. First in by being seen by that stupid girl back in the laboratory, and in not killing her before the alarm could be raised. Then in losing the chemicals in those beakers. And finally, by losing the specimens that they had been told to take from the lab.
All of it gone. All of it lost.
The ninja jammed his hand into the storm drain, trying desperately to loosen it — perhaps he could salvage one or two of the turtles if he was fast enough. The rat surely couldn't have eaten all four by now. But the drain was embedded in solid cement, and didn't budge an inch. All he did was injure his fingers, which were already bruised from attempting to cut through the curb a few minutes before.
A siren grew louder, and passed by directly outside the alley.
"We have to disappear," the injured ninja said tautly.
His partner gritted his teeth and rose to his feet. He knew he was right — there didn't seem to be any way to get to the turtles, and the green ooze was beyond any kind of recovery. All they could do now was return to the Foot Clan, and confess their failures. Perhaps Master Shredder would be in a relatively forgiving mood…
Then something caught his eye — a faint flapping motion in the shadow of some garbage cans. It was one of the turtle hatchlings, still smeared with the green ooze that lay in a filthy puddle on the alley floor. Its small head flailed to and fro as if in a panic, and its tiny flippers fluttered wildly against the ground as it tried to crawl away from the human looming over it. He could almost hear it screaming from fright.
"Is that one of them?" the injured ninja asked, blinking through the blood on his face.
"Yes — it's one of the turtles," he responded.
He carefully lifted the tiny creature from the ground, and slowly turned it over to check it for any wounds. He couldn't see any damage to its tiny shell or plastron, and it didn't seem to be bleeding. It seemed healthy enough — certainly it was energetic, the way it was flapping around. The only problem was that it had been splashed by the green chemicals, which still glowed faintly on its tiny body.
"We'd better get it back as quickly as possible," he said, slipping the turtle into a fold of his shirt. He could feel it fluttering wildly, like a trapped butterfly in a net, and it continued to do so until they returned home.