A/N: First off I would like to say thank you to SleepingSeeker who allowed me to do my own version of a sequel to her story 'What makes a father'. SleepingSeeker plans on having her sequel out some time this year.

This story will be extremely dark, darker then anything I have written, there will be mentions and talks about rape, and abuse.

It is AU and continues along the same lines with the same characters from 'What makes a father'.

Leo is 14, Raph 13, Donnie 11, and Mikey 9

Disclaimer: I do not own Scrag, or anything associated with the story 'What makes a Father'. This is just my take on the sequel to the story.

A/N2: I am not going to use italics for flashbacks, I agree with SleepingSeeker on they can be annoying to read, and you all are intelligent enough to figure out when you are reading a flashback.

It had been 3 years since Splinter rescued the four turtles from the hell that they had lived in. Scrag was now gone, the hated black rat though lived on in the turtle's dreams.

Many nights after their rescue Splinter would hear their despair as they often cried out in their sleep. Mikey had the worst of the nightmares, there were many nights Splinter would hear the 9 year old sob in his room.

In the years that followed the turtles learning martial arts, their night terrors slowed down but were still there to a point, some nights were better then others.

Splinter knew that this was not going to be easy, but he knew he had to teach them to trust, that was the big thing. Trust was the top issue for these boys, if he had to correct them while training they would often freeze or become frightened.

Splinter stood on the side and watched the now teenage turtles spar, he tapped his cane on the ground and said firmly.

"Yamete!"

The turtles stopped and turned to him, seeing the looks on their faces told him he had once again startled them.

"My sons, you are all doing exceptionally well. I am very proud of all of you."

Leonardo looked over at his three younger brothers and smiled at them, he agreed they had been learning quickly and at a wonderful rate.

Splinter approached his four sons and placed a hand on Leonardo's shoulder, the young teen no longer flinched when touched and Splinter smiled down at him and said to them all.

"I thought today we would do something different."

Mikey looked over and asked.

"Like what Sensei?"

Splinter put his hand behind his back and walked back and forth in front of his sons saying gently.

"As of today, it has been 3 years since I brought you four to his place and began raising you, it has been a journey my sons, but a fulfilling one at that. How would the four of you, like to go to the surface?"

Raph perked up at the sound of this and asked cautiously.

"Why? Where will we go?"

Splinter knew this son, had been harder to reach, Raphael remained cautious, and often angered easily.

"Raphael, this is more of a way four you all to get some fresh air, and exercise, if you do not wish to go... then I will not force you. But it can also be a training run too. You must learn what goes on above ground."

Donatello had remained the silent one of the group and was still startled easily, he never truly looked into any one's eyes and often avoided speaking unless spoken too directly.

Donnie looked down and asked in a quiet voice.

"Can we... can um... can we um... go to the junk yard?"

Splinter walked in front of him, he noticed Donatello shied away from him slightly and said.

"I will be coming along with you."

Leo told their father.

"Dad, can we go to a different junk yard..."

Splinter looked confused, this was their first time of going out since they arrived.

"What do you mean my son?"

Raph answered.

"Uh... the black rat... Scrag... he um made us go to this junk yard north of town..."

Splinter nodded his head in understanding, he never went to this junk yard since it had humans there and dogs.

"I never go to that one my sons, the one your brother asked about is east of town. This is where I found those books for him."

Leonardo frowned and shared a confused look with Raph.

"We don't know where that one is?"

Splinter smiled and said.

"Yes I know, this is why I am going with you, so you do not get lost, and the answer is yes Donatello."

He saw the boy smile slightly, Michelangelo stood silently by Raph and was nearly jumping for joy at the chance to go to the junk yard, a new one at that.

Donnie raised his head to meet his father's eyes, it was rare but it did happen.

"Are... we um... scavenging for something we need? Or can we look around for fun?"

Splinter walked back to his most gifted son.

"Is there something you need Donatello?"

Don looked over at his younger brother and then back to their father.

"Mike and I, we saw through a grate a while back some kids skateboarding... we were hoping that we could um..."

A smile came to Splinter's lips and he said.

"Yes Donatello, you and Michelangelo may look for a skateboard."

Both of the youngest turtles got excited, Raph asked.

"When are we going?"

Splinter told him softly.

"After night fall, I would like you all to get some rest, it takes a little while to get to the east side junk yard and I want you all to be on high alert."

They all stood up straighter and said in unison.

"Hai Sensei."

They all started to walk out of the dojo, Splinter spoke.

"Leonardo, may I speak with you?"

Leo stopped and turned to his father, he looked over at his brothers who no longer hesitated when asked to stay behind.

He walked over to Splinter and said.

"Yes father?"

Splinter walked over and shut the dojo doors, turning back he wasn't sure how to break the news he had found out days ago. He knew he had to tell the boys sooner or later. But he didn't want them afraid to go above ground now that they were older, and were not as skiddish as they had been before..

Inhaling deeply he said.

"Leonardo... I, well, a few days ago... I was listening to the news, they talked about a lab accident that occurred three years ago... just after you all came to live with me... it was the lab Scrag was taken too."

Leonardo visibly tensed at the mere mention of that nasty rats name, he felt like his insides were going into jello.

"Is... is that why we are going?"

"No, well sort of, I want to check it out... and I want to make sure that he really had been destroyed by humans... but I am not as young as I used to be. I know this will be hard my son. I do not want to put you all through this. But I have to know he is not still around. He knows these sewers, I don't want to risk him finding us."

Leonardo felt like his legs were made of led, he asked.

"What do we do if we find him?"

Splinter choose his words wisely and said.

"We can hope he is not alive. But if he by chance is... we will do what it takes to protect this family my son."

Leo looked back to the dojo door.

"What about them? Should we tell them?"

Splinter shook his head.

"No, I do not want all four of you to worry needlessly. Now listen, if you feel your self freeze up if we do happen across him, remember your training and stay strong."

Leo stood up straighter and said.

"Hai father, I wont let you down."

Leonardo went to his room after the talk, even at the age of 14 he was scared of the black rat he had once called father. He could not help the feel of dread creep into him as his eye lids closed.

The sound of footsteps were enough to make Leonardo flinch, he looked over and saw Scrag standing there with his arms crossed.

"What the hell Leo? Why is Raph not in here making my dinner?"

Leo looked up at him, but wasn't he just in his bed in the lair?

"Raph's in his room? We don't live here no more!"

Scrag back handed Leo and sent him to the floor.

"Of course you still live here you little shit! Why do you think your here? Besides if you ever think you can get away from me you have something else coming! Besides you like our little games Leo, I know you do. I hear your screams when we play our games."

Leo could feel pain shoot through his lower region at the mention of their games... Leo could feel tears running down his face as Scrag came up to him, he smelled the horrible smell that always came from Scrag when he was wanting to 'play' their game.

Leo shot up in his bed breathing heavily, he was covered in a thin sheen of sweat as he pushed the blanket off of him.

"Get a grip Leo... its only a nightmare. He's gone."

There was a knock on his door and Raph came in, the worried look on his face was all he needed to know that he had cried out in his sleep again.

"There back ain't they? Those dreams you were having? What triggered it this time?"

Only by accident did Raphael learn of his brother being raped by their father Scrag all those years ago, Leo had been crying in his sleep and Raph heard him scream for Scrag to stop...

Raph shook the memory away and said to his older brother.

"Leo, he's gone, and Masta Splinta wont ever hurt us. He has proven that many times."

Leo nodded and looked down at the bed below him, he looked into his younger brother's green eyes and said.

"Raph... what... what if he isn't gone? What if he is alive?"

Raph frowned and sat on the end of Leo's bed.

"What do you mean? Did Splinta say somethin when you stayed behind to talk?"

Leo looked around his room, he shared with Donnie since non of them seemed to be able to sleep with out at least one brother near by. He wanted so bad to tell Raph what Splinter told him but he was afraid to. Afraid he would be punished if he went behind his father's back and betrayed his wishes.

Since it was taking so long for Leo to answer Raph told him impatiently.

"Look Leo, don't tell me... but if he is back... what will we do? Can we really fight back against some one who is THAT much stronger then us?"

Leo looked deep into his younger brother's green eyes and said firmly.

"Raph, we are trained ninjas, we carry weapons on us. I think we can defend our selves against that bastard."

Raphael knew his brother was serious if he used foul language.

"OK, well Splinter says its about time to get going, better grab your bag and swords bro."

Raph stepped over to Donnie and shook him slightly.

"Hey Don, dad says it's time to wake up."

Donnie shot up, and for a moment there was a panicked look about his features, once he realized it was his older brother he calmed down and said softly.

"OK." He then followed the other two downstairs where they met up with Splinter and Mikey.

Splinter lead them down the tunnels into the deep part of the sewers, he looked back to make sure his sons were following close behind. He noticed Mikey was looking every where but ahead and said to him sternly.

"Michelangelo, you need to pay attention to where you are going my son."

Mikey jumped a little and ran ahead of Donnie who was already nearly taking up the rear of the group.

Leo looked back from where he was beside their father, with Raph directly behind him.

Splinter stopped when they got to a ladder, he noticed Leonardo's hesitation as he began to go first. Placing a hand on Leonardo's shoulder he said.

"My son, let me go first, that way I can make sure there is no danger."

Leo and Raph looked at each other puzzled, it had been years since they had been to the surface but the times they went and Scrag was with them, they were made to go first. This was something new to them.

Leo stepped back to allow their father to go first, Leo went after him followed by Raph, Mikey and Donnie taking up the rear. They were about 6 feet off the ground when Raph spoke quietly.

"Leo, come on bro, don't freeze up now, keep going."

Splinter looked back and noticed Leonardo was frozen in place.

"Is there a problem my son?"

Leo was clinging to the rail for dear life, his face had grown pale and he was visibly shaking. Splinter came back down a little and asked again.

"Leonardo? Is there a problem?"

Raph answered. "He's scared of heights."

Splinter looked down at Leo who was looking down at the darkness below and said softly and as gently as possible.

"Leonardo my son, listen to my voice, let the fear pass my son. I will not allow you to fall, you are safe my son."

Leo could hear Splinter's kind words but his mind was in other places...

"You pathetic little shit! Move your ass!"

Leo looked down at the black rat below and felt nothing but fear, he could see nothing other then his 'dad' in the darkness. Then he felt it, his body falling to the hard pavement below...

Splinter snapped his fingers and pulled his frightened son out of his hold on fear.

Leo looked up into the concerned face of his father. He felt like he was going to be sick.

"I'm scared..."

Was all he said before clinging to the bars for dear life. Splinter reached down and then hesitated I shouldn't touch him, he may panic more.

Donnie watched the scene above him and remembered the day that Scrag dropped Leo from the ladder because of his fear. He saw Splinter start to touch his brother then hesitate before bringing his hand back to the bars.

Splinter looked down at the others and said.

"Go back my sons, go back to the ground."

One by one all three went back to the ground, they looked up in the dim light as Splinter slowly got closer to Leo who was still holding on for dear life.

Splinter looked around at his surroundings and found a thick pipe running down the side of the stone wall near the ladder, he took hold and climbed down below Leonardo and said.

"Is that better my son?"

Leo locked eyes with Splinter and shook his head in a negative gesture.

Splinter knew he had to get his frightened son to move, he got hold of the pipe again and climbed up to where he was level with Leo and said softly.

"Leonardo, it is OK my son. I WILL NOT let you fall, I will catch you if you start to. Please let us climb up the ladder my son I am right here."

Leo had tears running down his face as he clung tighter to the bars shaking his head.

Donnie climbed back up the ladder and was directly below his oldest brother.

"Scrag, made Leo fall a several years ago. I don't know what he did, or how he did it but he made Leo fall down from the ladder. He wasn't hurt too bad but still it scared him."

Splinter sighed and said.

"Oh my son, here, why don't you get on my back and we will go up together?"

Leo shook his head, Splinter felt his patience going but tried again.

"OK then, lets go back down then my son. Can you do that?"

Leo nodded, it was the only positive move he had made this entire time.

Donatello got down and watched Splinter and Leo.

Splinter slowly followed his eldest son down the ladder from the pipe, once on the ground Splinter told him.

"My son, would you feel better if you and your brother's went first?"

Splinter was mentally kicking him self for not taking them out of the lair sooner, he would have learned of Leonardo's fear of heights long before. The young turtle could jump very high but now that he thought about it he never climbed or even tried to get to a high place.

Once on the ground Leonardo hid by the side of the ladder and said with fear lacing his voice.

"I-I-I'm so s-s-s-sorry d-d-d-dad..."

Splinter slowly approached him and said softly.

"My son, it is OK, I am not angry with you. I had no idea this entire time you were so afraid of heights."

Raph started to walk up to them when Leo stopped him, once he caught his breath and slowed his heart rate down Leo said more clearly.

"I'm sorry that I didn't tell you father... I should have... I thought I was over it after all this time."

Leo still hid beside the ladder, in the dim lighting Splinter could see the signs that Leonardo was not completely calm yet so, he kept his distance as not to completely frighten him again.

After a few more minutes Splinter asked him.

"Leonardo, you would not have been that scared if this wasn't a familiar location... have you been here before? When you were younger?"

Splinter noticed the far away look in those blue eyes and knew his son HAD in fact been here. A soft voice came up beside Splinter.

"Dad, this is where he used to bring us when we would have ta go get his food and stuff."

Splinter looked down at Michelangelo, and then back to his eldest.

"I should not have brought you four here, this is how I always went to go to the junk yard, tell you what lets go find another way up."

Leo jumped forward and said.

"No! Dad, can I try again? Please. I won't freeze up this time! I promise."

Splinter turned to the other three and noticed the forlorn look on Donatello's face and the sad expression on Michelangelo's.

Raphael spoke next.

"Leo, this ain't Scrag, you should know that by now, come on, lets just find another way up. It will be OK."

Leonardo looked over at his younger brother then back to Splinter, then with out warning Leo grabbed the rung of the ladder and hoisted his body up.

Splinter told him.

"Leonardo, you do not have to prove anything to me, come, let us find another way."

Leo shook his head and began to climb the ladder again, Donnie looked up at his brother and walked forward and took a hold of the ladder as well. He climbed behind Leo with Mikey following close.

Splinter went up next then Raph.

Leonardo nearly stopped again when he could hear Donatello's soothing voice say something to his brother and he kept going.

Once at the surface Leonardo's legs gave out and he sat on the ground as his family came up moments later.

Splinter stood beside Raphael for a second before kneeling next to Leonardo.

"My son, you did not have to do that. We could have found another way."

Leo was breathing hard still but slowed it when he looked into his father's eyes.

"I know... but dad, if I allow my fear to control me... then that means I am allowing Scrag to win. Raph's right, he isn't here any more, you are. Scrag can't control my fear of heights anymore like he used to. Like the time he pulled me off the ladder and dropped me to the ground, when Don tried to come to my aid Scrag told him he would suffer the same fiat, I heard him even though my ears were ringing with pain. I have to beat this father, I have to or else Scrag wins."

Splinter wrapped his arms around Leonardo and told him proudly.

"I am proud of you my son, and we will work on this."

Splinter let go and looked into his son's blue eyes.

"From now on, when I go scavenging, I will take you with me, so we can work on your fear."

Leo looked at his brothers then back to Splinter, an old fear bubbled up inside of his stomach, one that he had tried to push down and forget about.

Splinter noticed the way his son's body went ridged, fearing he had hit a raw nerve he looked to the other three.

Raphael spoke quickly.

"Can I come too? Please?"

Splinter felt that Raphael was trying to protect his older brother's fears so he said agreeing.

"Hai, you may my son."

Although it had been years, Splinter thought he had earned the boy's trust in him fully. Apparently he had more trust to build with these abused children.

"Leonardo, know that I would never lure you away to hurt you my son, you must know this by now."

Leo looked over at his immediate younger brother then back to their father.

"I trust you, its just... I keep having these visions when things happen."

Splinter nodded his understanding and said.

"Flashbacks my son, you have had them for some time now."

Leonardo frowned and asked.

"How did you know?"

Splinter smiled at him and softly said.

"I can hear you crying at night my son, you also talk in your sleep. I will not repeat what I have heard you say, but, if you ever need to talk just tell me my son. I am here, we have been over this. I knew when I took you four in that there were going to be a lot of healing on all of your parts. But I do not ever regret taking you in."

Splinter stood and told his sons.

"I think we need to get moving my sons, the junk yard is still a ways away."

Normally when Splinter would go to the junk yard he would go by rooftops, but, never fully knowing what Leonardo went through entirely with the black rat, the boy could not jump very well. Granted he could jump straight up in the air, but when it came to jumping across he would flinch in pain, when asked he would brush it off as nothing.

The five creatures moved through the night, going through ally's and finally making their way to the junk yard, when they got there the boys could not believe their eyes.

Mikey took a whiff of the air around them and said happily.

"It doesn't smell like sh-crap in here!"

Splinter looked over at his youngest and shook his head, for years he had been trying to control the foul language the boys had been allowed to use. There were slip ups once in a while though.

He chuckled and told his son.

"Yes, this junk yard does not supply food of any kind, this is a true 'junk' yard, there are no humans here so we are safe."

The four started forward when Raphael grabbed his two youngest brothers' by the shoulder and said quickly to their father.

"What about dogs? When do those come out?"

Splinter looked to the red clad turtle and told him.

"There are no dogs here my son, only a night guard that comes out around midnight to check things out, but even then he just waves a flashlight around then leaves. You are safe here to have fun."

Though it had been years since taking the boys in, Splinter still found him self reassuring them that no harm would befall them. This was something new, and no doubt there would be a new round of memories shared...

A/N: Whew, that has got to be a record for chapter ones for me! Nearly 4,000 words written! I would have to look but I don't think any of my stories have had long first chapters!

Let me know what you all think. And a special thank you goes out to SleepingSeeker for allowing me to do this! And remember she is going to have her sequel out some time this year!

This is my verson of 'What Makes a Father' Sequel, things are going to be different from the original because well for one I am not SleepingSeeker so I have no way of reading her mind. And two, I don't own the story line. So I am coming up with my own version.

Disclaimer: I Do not own Scrag, he belongs to SleepingSeeker! I am just borrowing with permission.

Also any mentions from 'What Makes a Father' belongs to SleepingSeeker as well.