Hey, all! Story two is here - this is where it really begins!

Don't own any turtles at all, let alone ninja ones.

One: Awake

He woke slowly, the pain in his head increasing as consciousness returned to him.

Black. Darkness.

…Are my eyes open?

They are.

The old, primeval fear gripped his heart in a vice. Can't see. Why can't I see? He stretched out a hand and touched cold, unforgiving concrete, then reached down to feel the unfamiliar clothes he was wearing. He was in some sort of cell, very likely with no means of escape. Is there anyone else in here?

'H-hello?'

'Mikey, is that you?'

'Raph!'

'Hey, little bro. Where are you? I can't see a thing.'

'Over this way. You can't see either? What's going on?'

'It's not just me?' Raph heard his little brother scuffling toward him. 'How dark is it? Or have we gone blind?'

'Can't be that. I'm starting to see stuff, bits of light. Must be only temporary.'

'Do ya know where the others are?'

'No.' Mikey inched closer to Raph, who put an arm around his shoulders, trying to comfort the younger turtle. 'I'm scared, Raph. Where'd they take us? Where's Leo and Donnie?'

'It's okay, Mike. We'll figure this out.'

They were just able to discern shapes when there was a familiar-sounding groan from the far corner. 'Ow. Did anyone else see that truck?'

Raph would know that voice anywhere. It lectured, scolded, and argued often enough, but right now, it was the best thing he'd ever heard. 'Leo! Are you okay?'

'I think so, but I can't see anything. And my head feels like a house got dropped on it.'

'They did hit ya with a huge amount of tranq' darts. More than they'd normally use, I'd guess,' said Raph.

'Sorry,' said Leo, still sounding rather dazed. 'Mental blank here. Can we just go through everything that happened while I wait for my sight to return from its holiday?'

'Okay. I got knocked out pretty early on, though,' said Mikey. 'Raph'll have to continue from there.'

'No prob. Start from the beginning, Mike,' Raph replied.

THREE DAYS PRIOR…

Four shadows leapt across the New York rooftops. The rain was beginning to fall, a welcome relief from what had been an unusually warm day. It was a full moon, which meant extra caution had to be taken to avoid being spotted. And with gang activity on the rise again, it was pretty clear that if they put a foot wrong, the hunters could quickly become the hunted.

Raph and Don had returned from a patrol the night before with some interesting information. They'd discovered where the weapon shipments the Purple Dragons had been receiving were ending up – and who they would eventually be sold to.

'They're tag-teamin' with the Foot again. An' here we were hopin' the You-Sucks-Clan was out of it for good,' Raph said, showing them the pictures they'd loaded to Don's computer – Purple Dragons loading the crates of ammunition into a large truck, watched by the silent, inscrutable ninjas, the emblem of the Foot Clan prominent on their shinobi uniforms.

'Why do they keep coming back?' grumbled Mikey. 'We just kick their butts again, so why do they bother?'

Leo frowned. 'Because, Mike, there are so many of them that they reckon one day they'll get lucky and kill at least one of us, which they hope will make the team fall apart, ergo effectively making us less of a threat and easier to neutralize. Why do you think they go out in small armies? There's about thirty Foot per patrol now – and that's a small group.'

Don caught the worried tone in Leo's voice and looked up at his eldest brother, noting the concerned frown and body language that was practically yelling "NERVOUS!". Was Leo afraid of a few Foot Ninja? Raph and Mikey were also confused. Their big brother had become so paranoid.

Little did they know.

In hindsight, with all the noise the PDs were making, it should have been pretty obvious that Leo had a right to be feeling nervous. Of course, in reality they only realised it was a trap when the tranquilisers started flying.

Mikey was the first to go down, hit from behind by half a dozen darts. Don, running to help, took a sword hilt to the back of the head, knocking him unconscious immediately. Raph shoved Leo out of the way as another volley of darts flew past, taking several shots in the arm. He wavered a little, but continued fighting. Eventually he couldn't battle the effects of the sedative any longer, and he sunk to the ground.

The last thing he heard was Leo's cry of pain and the thud of darts hitting skin. Six, seven, eight – then he blacked out and heard nothing more.

'All in all, that fight only lasted about fifteen minutes,' said Raph. 'Record fail, I think. Usually we'd have put up more of a fight.'

'Well, we haven't exactly been ourselves lately,' replied Mikey.

There was a silence. Master Splinter had died peacefully in his sleep earlier that month, and the turtles were still dealing with the grief.

Raph squeezed Mikey's hand, trying to offer some comfort, and was surprised when his brother froze, startled. 'Mikey, what's the matter?'

'You have five fingers.'

'Wait – so do you!'

'Guys…'

They turned to look at Leo, who was staring at them with an expression of mingled disbelief and fascination, an expression which was soon echoed on the faces of his younger brothers.

'Leo -'

'Guys, you've got –'

'– You've got –'

As one, their hands flew up to touch their foreheads, meeting an unfamiliar sensation. 'HAIR!'

They freaked out for a few seconds, before moving around to observe what changes had occurred. As well as humanoid hands, their feet now had five toes and were distinctly more – well, foot-like. The strangest and most disorienting transformation was their shells.

Moving around with two-thirds of your own weight on your back for your whole life makes for some interesting alterations in balance and agility when that weight is removed. On closer examination, Leo pronounced their new 'evolved' shells to be nothing more than a natural bullet-proof vest. Flat against both their back and front, it would certainly make the wearing of disguises much easier. With their faces and green skin covered, they would look perfectly human.

'Well,' said Leo once they had all calmed down, 'Don's going to enjoy testing all of this when he wakes up.' He looked around, sensing that something wasn't right. '…Where is Don?'

Then the door burst open and a scientist-type man walked in, followed by six heavily armed guards. 'Bring the blue one. We're done with the others; they aren't suitable for the third stage. You can get rid of them.'

One of the guards hit Leo with a stunner, then he and another guard picked the unconscious ninja up by the arms and followed the scientist out. The four remaining guards raised their tranq guns. Raph gave Mikey's hand one more reassuring squeeze before the darts hit and they blacked out.