Prologue – Nucleus

Not so far under the streets of New York, in a sealed-off passage that used to be a pedestrian walkway, four very unusual turtles are hard at work under the watchful eyes of their rat father.

"Done!" Raphael shouts. His pencil clatters down onto the table.

"Done!" Donatello calls an instant later, and tries to shove his paper in ahead of Raph's.

Splinter takes both papers at the same time, and looks them over. "Very good," he says. "You may go play."

Leonardo looks up from his work with jealous eyes, then taps his pencil against his beak and writes down another number.

"Can we go sit under the grate?" Raphael asks.

Splinter nods. Raph hops to his feet and pads towards the door.

Donatello leans over Mikey's shoulder, jabs his finger at one of the problems, and whispers, "It's an eight."

"Donatello!" Splinter says sharply. Donnie looks at him guiltily, then jumps up and follows Raph.

Michelangelo frowns and erases, leaving a big smudge over his work.

Raphael reaches up and opens the door, waiting while a dozen or so of the lair's resident rats troop in, then looking both ways before leading his younger brother out into the tunnels. The two Turtles splash along the passage until they reach the grating in the ceiling, under which they are permitted to sit quietly and absorb the sunlight that is so vital to their health.

They perch on the thick pipe running along the wall, and raise their faces to the warm light.

"Those problems were too easy," Raphael says.

"Way too easy," Donatello says, one-upping him.

"Super-easy," Raph says.

"As easy as - as..." Donatello struggles to think of a comparison that can't be gainsaid. "As holdin' your breath a long time."

Raphael is forced to concede. Not only is breath-holding really easy, Donnie is the best at it.

For a while they don't say anything.

"Y'ever wonder what's up there?" Raph asks, nodding up at the grate.

"People," Donnie says off-handedly. "Buildings. Cars."

"I mean," Raph says, before Donatello can list everything in New York, "d'you think it's like Sensei says?"

Donatello tilts his head and looks at him.

"Like..." Raph thinks for a minute. "D'you think all humans are nasty, like he says?"

Donatello raises his eyes thoughtfully.

"'Cuz," Raphael says, "all the mutants we know are nice people." He shifts. "Most of the time. So it'd be... it'd be weird if all the humans aren't nice."

"I think we should go in now," Donatello says. He slides down from the pipe and looks at Raphael expectantly.

"You go," Raph says. "I'm gonna stay a few more minutes."

Donatello goes.

Raphael looks up at the grate, and wonders.

When Donatello returns, Splinter is patiently repeating his lesson on how to trade numbers from one column to another. He writes down a problem for Leonardo and Michelangelo to ponder, then looks up. "Where is Raphael?" he asks.

"He's coming in a minute," Donatello says. He steps out of the wash bucket and scuffs his feet on a towel.

Splinter nods, and encourages his less mathematically-gifted sons to work out the answer with bottle caps.

Half an hour later, Raphael has not come.

Splinter dismisses Leonardo and Michelangelo from their lesson, and leaves them to play with Donatello. He slips out of the lair, and quickly makes his way along to the grate.

Raphael is not there.

Not in the very small area he is allowed to explore on his own.

Splinter races back to the lair and snatches up the old raincoat he uses as a disguise. "Stay here," he orders the three startled Turtles, layering the command with as many dire overtones as he can manage. "Do not leave."

As he whirls on his coat, he notices a handful of rats watching him curiously. "[Look for my son!]" he shouts at them, as loudly as he can in the subtle language of his birth. "[Tell the whole colony to look!]"

Without pausing to see whether his instructions are being obeyed, Splinter rushes out into the sewers. He goes back to the square of sunlight, and inhales deeply, searching for Raphael's distinctive scent. There. He follows the trail to - no - a ladder. He climbs rapidly, lifting the manhole cover and slinking out into the alley. The scent leads him to the edge of the sidewalk, where - no! - it becomes muddled, mixed with smells that are not of his family. He tries to follow, keeping his head down and face covered, but it quickly becomes impossible.

He retreats to a shadowed corner, gathering his thoughts. He makes one more attempt, but Raphael's scent is a mere phantom now. He can't be sure whether it's real, or a product of his frantic imagination.

Everything in him wants to keep looking, but his search now will be random at best. He will not find Raphael this way, and will only put himself in danger.

He needs to go home, to protect his other sons, and form a plan.

He makes himself do it.