Someone asked about the timeline. To my recollection the pulse occured in 2009. And Dean karked it '08.
However, as far as being set is concerned, these first few chapters are pre-pulse (post Dean's death), and then it'll shoot forward through S1-2 of Dark Angel.
Hope that helps.
You Can't Hide
In the middle of the night, Ben woke to the harsh tug of his mother, telling him that they needed to leave. Right now.
Groggily, he began to ask why, when the sound of the front door being kicked in reached his ears.
Lisa's eyes widened and she pulled Ben into her arms, out of his room, and down the hall to her bedroom; the subtle sounds of movement downstairs could be heard.
Once inside, she opened the closet, and shoved her shoes aside to reveal a trapdoor that, from Ben's memory, was directly above the pantry, right next to the back door.
"Ben," his mum turned him to look her in the eye. "I need you do be very quiet, go downstairs, and when you get a chance, run. Run away."
"What's going on Mommy?"
"There's some men, and they want to take you. I can't let that happen. I love you Ben, please do this."
There was too much for him to process, but he did realise one thing was amiss. "What about you?"
"They're not after me, I'll be alright. Please go. I'll meet you at the park, hide in the tunnel." She pushed him towards the hole.
"No."
"Ben, we don't have time to argue, just do as I say."
Frantically, she pushed him towards the ladder. He'd always wondered why that was in the pantry.
When he'd climbed down, she shut the door, and he could hear her moving her shoes back on top of it.
He held his breath, and waited until he was sure the coast was clear.
Slowly, he pushed the pantry door open, and when nothing came oppose him, crept towards the back door.
He managed to get it open with only a silent click, and was sneaking to the back fence when he heard his mother scream.
He dropped all pretence at stealth. "MOM!"
He heard his mother yelling to run but he didn't care, he was going back in.
He made it to the door when two men, dressed in black had him against the wall and secured his hands. "Let me go! Mom!"
They dragged him to the foot of the stairs where a blonde man in a leather jacket descended. His eyes were severe as he appraised him.
"It's okay 493, we're going to take you home."
--
When he woke up, he was sitting in an office. A pretty lame office, Ben thought as he looked around. His gaze stopped on the man behind the desk.
"You're awake, 493."
He glared. "My name is Ben. Where's my mom?"
"You don't have a mother."
Ben snorted. "Everyone has a mother." Then considered. "Except for you. You probably have a bitch."
The mans' eyes narrowed.
Ben looked at him earnestly. "You know what that makes you?"
Choosing to ignore his comment, the man instead asked. "Did you ever find it hard to fit in? With school? With friends?"
Ben folded his arms. "No."
"Still," he continued, "you knew you were different. Faster, perhaps, than most kids your age. Stronger too."
Ben remained silent. He did know. He had better eyesight than all his friends, better balance, and could remember things almost mechanically. Most of the boys had called him a freak, only some thought it cool. The girls did, which was just fine with him.
"See, the thing is, you're not like most kids. You're special. This is a place for special kids, just like you. You were supposed to be here, but... unforseen circumstances didn't make it so."
"Where's my mother." It was a demand, not a question. One that gave the man no wiggle room to avoid answering, so he did.
"She's safe."
"Take me to her."
"That's not going to happen, son."
"I'm not your son. I want to see my mom."
"You can't. She's comprimised our entire operation. I'm afraid you won't be able to see her again. You belong here."
Ben stared back defiantly. "I belong with my mother."
The man looked at him for the longest time, before heaving a sigh. "You're can't go back, son. That's just facts. You'll have to live with it. But, as long as you stay here, I guarantee you that your mother will be safe."
Ben knew what they were doing, he wasn't stupid. Blackmail, pure and simple. "What if I refuse?"
"You don't have much of a choice, son. I'm sorry."
Ben exploded to his feet, his voice bouncing off the walls. "I'M NOT YOUR SON! AND I'M NOT STAYING HERE! TAKE ME TO MY MOM, NOW!"
Sighing, the man pressed a button on his desk, and two men entered. He nodded at them, and Ben felt something prickle his neck, before he fell asleep.
"Take him to psy-ops, tell them to scope it all out and bring him up to date with the others. Then put him in with alpha unit."
--
He'd been cleaned up; hair shorn, bland clothes. Then placed in psy-ops for three weeks, until he was "convinced" that his whole life had been a dream. He didn't believe them, but he didn't want to go back to the cute little girl who made his thoughts fuzzy, like she had stolen something from him. He wanted to go back to the other room even less, so he feigned innocence.
He'd been stationed in a unit of other kids, one of them had gotten "sick" and he was the replacement. His appearance made the others wary, and he later found out that it wasn't often that they met new kids their age. Or ever.
When the guards had left, Ben had told them his name. His real name, not some number they assigned him. He was Ben, and they weren't taking that away from him. He also said they should have one, too. When they looked to him, mixed parts eager and hopeful, he said that they deserved the right to pick their own name, "'cos you have to live with it, so you won't have no one to blame but yourself. Just don't pick something bitchy like Ryan."
As they mulled it over, he told them of home. Of a mother that loved him, and what a family is. He spoke of school, and friends, and parties and music. And each night when the guards had left he'd regail them with stories of life outside Manticore, of freedom.
Their innocence about the way things worked, prompted him to step up and act as the unspoken big brother. He looked out for them, kept their spirits up, and bonded with every one, including those that were weary of hearing things that clashed with what their commanders told them.
When it came time to tell them of the things that went bump in the night, he couldn't bring himself to say that there are bad things out there, things that want you dead for no reason than " 'cause". He didn't want to ruin the image of a wonderful place outside these walls. So instead he told them the story of a good place, and a bad place, and of monsters that became the 'nomalies.
One night, X5-433 - Jack - started seizing. They knew if he was caught, they'd take him away like the others, only this time they wouldn't be getting a replacement.
The door screeched and they ducked back into bed, feigning sleep as the cleaner approached Jack, and placed a picture in his hands.
When he had left, they wandered over to a now-lucid Jack, who was staring at the picture in awe.
"She's beautiful," Zack had remarked.
"Who is she?" Max asked, and they all turned to Ben for an answer.
Ben looked at the picture of Mary, and told them what he remembered from church. "She's watching over us."
It was some time later that they'd built a shrine on top of the wing. Baubles, trinkets and even lost teeth that they'd found adorned the picture. Because if they meant so much to them, then maybe it'd mean something to her. Ben started to push faith to them, not just because they needed hope, but because after nearly two years of this seclusion, he did too.
He was starting to break.
Though he hated this... institution, he learnt what they taught him. Fighting, tactics, what 'honour', 'loyalty' and 'discipline' meant, and what their purpose was. And if he disagreed, he learned very early on to keep it to himself, all the while trying to figure out a way to escape.
When they brought a convict in for one of their missions, they'd neutralised him with ease. And when they opened his shirt to reveal the tattoo, something in Ben snapped. A bleeding heart, that's what he had. A giant gaping hole where love should be, where his mom should be.
It wasn't until that night, when he lied awake in bed that he fully realised what he'd done, and it sickened him. He crawled into the bathroom that night and vomited up his dinner. But in the midst of this newfound disgust, he also strenghtened his resolve. He had to get out.
He had to.
Four days later, they escaped. And Ben went back to the only place he'd ever called home.
