AN:
Why Hello there, and as you can tell, this is a quick update, but then it did take me a while to write, but I hope you love. I am just getting my head around the dynamics of writing a fan fiction in this season. As I am going to have events in the final season, it will follow that plot, but as you guess changes are made with Lily involved, plus I am hoping to make it like the others. Adding scenes that weren't in the show.
I really am going to love writing this, and I can't wait to see more review XoXo

Chapter Two

While it was the graveyard shift, where most places that takes place in the night. Lily glanced around the club at one in the afternoon, the regulars who didn't have serious day time jobs, or just layabouts spending their welfare cheque.

While the dimly lit bar had just Lily sitting with an old man who was tending bar, she sat with a smoke looking to the stage with a girl who looked like a child. Her hand going to her hair thinking of Michael, it wasn't like she wanted him, but being left alone didn't feel right.

"So, why does a pretty thing like you waste your time in a dump like this?" Terry said to Lily while she played with her smoke.

Lily glanced up to the old man; she put the smoke out, "Well I'm not really sure." Her eyes going towards the door as it swung open.

Michael felt some relief, while the club didn't look any different in the day than it did at night; he closed the door behind himself. His eyes caught onto Lily, she looked surprised to see him, but she put out the smoke in her hand getting to her feet walking towards him.

It was strange to think of someone and then see them, Lily found herself standing in front of Michael, her eyes locked on his before her hand swiftly smacked him around the face. "You asshole!"

Touching his face, Michael blinked the confusion. "What was that for?" He asked feeling puzzled to why she would hit him.

"You left me, in my bed!" Lily shook her head taking his arm and dragging him through the club, she didn't want this to be said in the middle of her work. Even if she knew Michael wasn't fighting her, she pulled him into the female's toilet and locked the door behind them. "I can't believe you'd do that." Holding her hand up Lily looked livid. "No. I didn't expect you to do that to me!"

Michael kept touching his face, it still stung from the slap, but he exhaled a long breath, "Lily, last night…" He stopped seeing the hurt in her eyes. "I didn't want you thinking I used you."

"And leaving me alone in a bed just makes me feel very loved." Lily raised her eyebrow, her hand on her hip while studying over him. "I am not an idiot Michael, it's not like we're a in love married couple. We were both just looking for some escape, and you're not excepting the fact that Sara is dead."

"Is she?" Michael's question caught Lily off guard; he watched her studying over his face. "Lily, did you see the head?"

Lily took a step back, her hand going to her hair for a second. "I don't know." Her eyes were shifting from one point of the room to Michael.

"Did you see the head; did you know for sure that it was Sara?" Michael's voice more determined than ever to get an answer, a phone call with Lincoln didn't help, even if Michael left out the part that he knew where Lily was.

Lily shook her head, "I don't know. Michael I never saw it that long before Lincoln pulled me away from it, but that Gretchen made it clear that she killed Sara. And L.J…" She stopped talking. "Why are you questioning this?"

"I was close; I was very close to killing Gretchen." He exhaled, "And she, Gretchen told me that Sara was still alive." Michael now moved his hands going over his face, he tried to keep calm, but all he could remember was everything that happened that day. The conversation with Mahone, seeing Whistler being killed. He didn't care about the company; he just wanted to know if Sara was really alive.

"Well if I had a gun to my face I would say anything to keep my ass alive…" Lily waved a hand in the air; she could feel Michael studying her. She'd never thought she'd be having this conversation when she pulled him into the room, but now Lily stood still feeling her eyes pulled to his. "There is only one way to know for sure she's dead, and that is to find where she'd go."

"Chicago." Michael whispered, but he looked up to Lily, "But I have to get there without being spotted."

Lily brushed a hand into her hair, "Well I guess I can help, it's not like I have rooted myself here." She stepped forward, her hand reaching out to lightly touch where she'd slapped Michael. "I don't want what happened last night to change things between us."

Michael closed his eyes for a second; he brought his hand up to place it carefully over hers. The moment his eyes opened, he could see that she wasn't the same Lily from all them years ago. "I think things have already changed." He stepped closer, his arms wrapping around her, he pulled her into his arms holding her. "I need to know."

"I know…" Lily whispered, "And I will be with you." She pulled back, smiling her hand held out for Michael's. "We've got a lot of ground to cover to get us to Chicago."

Lily opened the passenger side door, she knew the area Michael chose to park, but she exhaled looking around them carefully before putting some dark tinted sunglasses on. "I hope you know what you're doing Michael, you're still a wanted man here." She kept looking around herself, because in reality, she was also wanted.

"I know what I am doing, I just need to speak to Bruce, and he'll know where Sara is. If I know Sara, He'd be the first person she'd ask for help." He kept walking with Lily rushing behind him.

Lily didn't really know anything, maybe it was them few days where she was in hiding, and Michael and Lincoln were running around trying to find a way to clear Lincoln's name. "Well that, or maybe she's really dead Michael, and you're in some deep seriously fucked up denial." She paused as Michael walked out in front of a cop car; she froze and rushed after Michael when it drove on. "And you're going to be spotted!" She snapped getting his attention finally.

"Why are you so determined to think Sara is dead, for all we know Sara could be out there scared." For a second Michael could see Lily's face falling, he closed his eyes pinching the bridge of his nose. "I just need to know!"

Lily now stopped with Michael at a pay phone; she tapped her hands on the box watching Michael pick up the phone, and then put some change into the machine. "You know with cell phones, it's a lot less noticeable than a pay phone in the middle of a crowded street."

Michael dialled the number ignoring Lily, he listened to the phone ringing, and he took a second to see Lily looking out for him. "A cell phone can be traced, and this way if Company is listening onto Bruce, they can't find me." He exhaled, but listened to the ringing phone.

"Right… The company." Lily Turned her back on Michael now starting a conversation she didn't care about, her eyes kept looking around, but froze seeing the police cars.

"Michael…" Her voice soft, she lightly pulled on his jacket, for all sense and purposed she wished he never picked out to wear. She felt a lot better in a pair of jeans and blue blouse covered in a old looking hoodie. "Michael we need to…" She paused seeing the officers to close to get away from.

Michael froze seeing the police. "Are you Michael Scofield?" one of the officers asked, and Michael looked to Lily seeing she was already being cuffed. "Are you Michael Scofield?!" This time it was more demanding, and Michael kept the phone to his ear.

"Yes." Michael now hung up the phone feeling himself being put into hand cuffs, he side glanced to Lily as if to say sorry, but all she could do was shrug.

Donald Self stood outside the integration room, he felt like static energy was running through him. How long he'd waited for this, and finally it was closer to his grip. This was everything, and as time was precious, he glanced into the room seeing Michael Scofield sitting at the table; by the window looking out into the world was Lily Carlin, also Michael's wife. In his arms was a folder, and when he finished this conversation, he was going to have his way.

"You should relax." Michael turned to look at Lily standing by the window biting her fingernail.

Lily's eyes snapped to Michael, "I am deeply sorry, but I am not really ready to relax, I am facing serious time." She shook her head. "This was so not what I signed up for."

"And what did you sign up for Lily, you ran away from Linc." Michael felt his eyes going to the table. "I didn't expect this to happen." He brushed his hands over his head remembering that night. "You were meant to love him…"

"Michael." Lily moved from the window to the table, she placed a hand on his shoulder, but before she opened her mouth, the door finally opened and a ginger haired man walked in.

"Michael Scofield. I'm special agent Don self, homeland security. Were you there when James Was killed?" He asked avoiding the glares that Lily was giving him.

Michael glanced up to the agent, "I didn't kill him." His voice dead serious, but then he didn't understand what was going on.

"I know you didn't." Donald was looking from Michael, and then to Lily standing behind Michael looking very frustrated with the situation. "He was a independent contracted who was working for the company for ten years." Donald got up getting some cups; he put the three of them in a row pouring out coffee. "He was assigned to find Scylla once it went missing." He walked to the table putting a coffee in front of Michael and Lily, "you know what Scylla is?"

"It's the company's little black book." Michael replied, he looked to Lily playing with a coffee cup, he knew that from her expression she'd had enough of the company taking over her life.

Donald kept his attention on Michael, "He was going to make a copy of it, and give it to me." He finally said.

Lily exhaled, "So what do you want from Michael then?" Her eyes locked on to Donald's, and she felt like she could pretty much just do her time, she was done with all this crap.

Donald laughed to Lily, "You're looking at major time, you know I'm right." He kept talking to both Lily and Michael. Donald sat down slowly, "How would you like to walk away from it all, and not do a day?"

"In exchange?" Michael asked, he knew this was going to be something he didn't really want to do.

Donald looked excited; he leant forward, wanting to keep both of their full attention. "Scylla !" He broke into a big grin.

Michael started to lean closer, he could feel this need building, and he knew it was time to make a negotiation. "Right. Sara Tancredi. Last seen in Panama, you help me find her. Then we've got a deal."

Lily rolled her eyes, but lucky for her Michael didn't notice, but Donald did. "She's not my department. Scylla is." Donald didn't know what else to say.

"Then find it yourself." Michael snapped back, he really didn't care; all he wanted was to know where Sara was. "Looks like the government should have a little more reach, other than someone facing major time."

"For an operation this size, it would need a signature from twenty different department heads, what a bet at least one of them is company." Donald said, he really needed this to work, he had come so far, he couldn't fail now. "The only way this is gonna work is via freelancer, off the books."

"Sounds complicated…" Michael pointed out. "I'll pass." His words were as blunt as he could make them. But then he side glanced to Lily and wondered about her, but her hand came up touching his, so he knew she was behind him.

Donald looked from Michael to Lily and back again, "I am giving you an opportunity to avoid fifteen years in jail, not to mention the time your brother is facing."

Lily suddenly felt a lump for in her throat, her eyes going from Michael's hand under hers, to Donald. "What!"

"What are you talking about?" Michael felt as confused as Lily looked.

"The company tried to take him out in Panama. He, um… Reacted, apparently." Donald felt he needed to put this out, he now glanced to Lily looking white as a sheet. "But I just made a deal with the Panamanian authorities so he can do his time in the US. He should be touching ground any time now." He smirked looking to Michael. This was the string he needed to pull to get his way.

Lily felt her hand let go of Michael's, she glanced to Donald putting a big file on the table, he then pulled out a piece of paper holding it up to Michael, and finally it all clicked to Lily. "Shit!" She snapped feeling Donald looked at her.

Then Donald looked back to Michael, "You recognize this handwriting? It's your fathers." He spoke seriously, and he could tell from the look on Lily's face she knew what was going on. "He spent the last two years of his life going after this very thing." He passed the piece of paper to Michael, he watched as Michael stared at the piece of paper with Scylla written on it. "Do you believe in fate, Michael?"

"I think I'd like to talk to my brother…" Michael finally said looking back to Donald, he felt like this wasn't going to be so easy to get out of now.

Donald now got to his feet, he glanced from Lily to Michael again, "As soon as he arrives, you'll be able to talk." He pushed the folder forward. "You're not leaving this room, and I have officers outside, so no funny business." Donald got to his feet heading out of the room.

Lily exhaled, "Michael, this shit is serious." Her voice a low whisper, she didn't know if he was still outside, but then again they could be recorded right now.

"What do you mean; you act like you've seen this before?" He held the piece of paper up, and she took it from his hand. "Lily, what are you not telling me?"

Lily got to her feet again; she glanced over the word, and then tried to go back to being in hiding, helping Jane. "Scylla ," She exhaled trying to think of the right words. "When I was with Jane, the woman who worked with your father… I asked if there was anything I could do to help. That was when I started to try and find anything I could about Scylla , and I never got far, because that was when I found Linc to be exonerated, and I had to find you both."

"So you're saying is that this is something that will take the company down?" Michael reached for her hand touching it softly.

Lily's eyes went to Michael's hand, then back to his face. "All I am saying is that I don't know." Her voice calm, but deeply she wished she knew more. "But it's what your father was doing."

Being back in the states felt weird for Lincoln, after being in Panama for nearly five months, it didn't feel right. But that he never thought he'd be arrested again, he thought about all the things he was doing in Panama.

He liked Panama, even after the escape, after Lily leaving him. It was just going to be himself and L.J. Yes Sofia was helpful, and a part of Lincoln knew that Sofia wanted more than friendship from him, but he just wasn't ready to move on from Lily.

While the drive seemed long, Lincoln could only think what Lily was up to. Where was she? Was she moving on with her life? Did she find someone new?

All the questions made Lincoln feel sick, he hated time alone with his thoughts, he hated that even in the night before falling to sleep, and he would reach for a body that wasn't there. Stuck with thoughts of her was all he could do before sleep would eventually take him.

So as he pulled up to the station, he glanced out the window to see Michael standing by an agent, but looking to his brother was short lived seeing her standing the other side of the agent. He felt suddenly worried, but he watched the door open, he was Y cuffed, so as he walked into the sunlight, he could tell this was going to be harder than he could imagine.

Michael took the first step forward, he'd not seen his brother in so long, it was weird seeing him again. He glanced back to Lily seeing her biting her thumb, it seemed it was not easy for her to see her ex.

"Hey…" Michael looked over Lincoln's face; it was seeing the Y cuffs, and then turning to face Donald. "Is this necessary, he won't run."

"Uncuff him." Donald commanded, and the cuffs were taken off. Lincoln used this time to wrap his arms around Michael, he held tight before letting go.

Michael smiled, "You couldn't keep out of trouble?"

"I can't help but attract it man," He then turned to see Lily still standing still, "When did you find her?"

"It's a long story…" Michael glanced back to the building, "But there is something I need to show you." He added while walking with his brother to the building. Michael glanced over Lily to see her face, it seemed like none of them were expecting to see Lincoln, and know how to act.

Lily kept behind Michael and Lincoln, she felt weird seeing them both together, or maybe it was going to be hard for her to speak to Lincoln. The last time they spoke was when he walked out of her life. She didn't even know if he wanted to have her speak to him at all. All she knew was standing in the room, she stood back, the conversation wasn't something she was following, but all she could guess was it had a lot to do with Scylla .

Lily snapped when the door knocked, she looked up to see Donald leaving the room, so she now felt her eyes going over the back on Lincoln's head. "If we take this deal, after this is done, you can look for Sara… if she's still alive."

"If we take this deal, we can be dead long before I get the chance Linc." Michael sounded worried, and when he sounded worried, it made Lily feel nervous.

The door opened breaking the awkward silence in the room. "You guys must have some big time friends." Donald said walking into placing some papers down.

Lincoln looked up, "What you talking about?"

"Someone just posted a significant amount of bail for the three of you." His eyes going around the room.

Michael looked confused, "Who?" He now glanced to Lily still standing by the window away from Lincoln, and he wondered how awkward this was going to be.

"I don't know, but they're outside, you're free to go." Donald sounded seriously pissed off, and while Lily took a step to get closer to the door, he exhaled. "Take this file, it has my number inside."

Lincoln took it, he looked to Donald, then the file again. "We're not doing this."

"This file, it means nothing to me anymore." Donald turned his back on everyone, he felt like he was banning on a brick wall, it wasn't fair.

Michael felt Lincoln and Lily behind him as he walked out the room, another agent lead them to a door, and as Michael slowly opened it up, he glanced in to see a man waiting for them. "Bruce Bennett." Michael said out loud looking surprised.

"Let's go for a drive." Bruce smiled, he looked over Michael, Lincoln and Lily, and he knew this was important.

Michael exhaled, "Yea…" He let Bruce walk out of the door, he started to follow. Even as they all got into the car, it seemed like everyone in the car didn't know what to say. It wasn't a long drive, but as they got closer, it seemed they were heading to a house, and Lily kept close to her side of the back seat.

Lincoln could feel tension, he wasn't one for filling awkward silences, but every now and then he'd steal glances to Lily. She'd changed her hair colour, it was weird seeing her without her trade mark dirty blonde hair, but she was still in a bad habit of biting her thumb when nervous. Lincoln couldn't help but notice she'd lost weight over the months, her eyes blank as she stared out the open window.

Lily waited until everyone else got out of the car, she felt like something important was going to happen, this was strange as she kept her distance from both Michael and Lincoln, but getting inside the house she held the Scylla file close to her chest.

Bruce walked them to a room, and while Michael felt nervous, Bruce opened the room for them to walk inside.

Lily felt the file slip from her fingers, it was like seeing a ghost. A ghost that made her stomach knot up, and as Michael moved quickly towards the sight, Lily couldn't help but know deep down this was really happening. Sara was alive, and Michael was holding her in his arms, he kissed her and Lily quickly picked the file up and headed to another room.

Sitting at a kitchen Table Lily felt grateful for the change of clothes, sitting in a pair of yoga sweats, a long vest, her hair was pulled into a messy bun looking over the file. Each piece of writing was either something she read before or something new. Her glasses falling down her nose she pushed them up trying to work something out.

"You hungry?" Lincoln walked into the dining room, he was holding some boxes of Chinese food, and he could see she was deep in thought.

Lily stopped reading; she placed the piece of paper down, her eyes going from the food, to Lincoln's face. "Not much," She tried all she could to keep her voice even. When she glanced to the other room, she didn't want to know what Michael and Sara were up to, but she moved some papers about to have space at the table. "But sit if you want."

Lincoln placed the food on the space made, he opened a box, and then he pushed it in front of Lily. "You've not eaten all the time we've been here, you've got to eat something Lil…" His voice comforting, but then it was hard for him to look at her without feeling some kind of sting in his chest.

"I…" Lily found the chopsticks by the box looking into it feeling her stomach rumble, "I guess you're right." She now started to eat looking back to Lincoln starting to eat to. "So how was Panama?" Her voice was aloof.

"It's okay, was in the middle of starting a dive shop." He played with his own chopsticks; he glanced up to watch Lily starting to eat. "What have you been doing?"

Lily shifted her weight on her chair, her eyes going from the Chinese to Lincoln; she found it hard to look at him in the eye. "Just living in LA, I was doing some waitressing." Her fingers fiddled about, but felt her hand reach up scratching the back of her head. "Nothing exciting."

"Oh…" Lincoln now didn't feel so hungry. "Were you seeing anyone?"

Lily put the chopsticks down; she didn't know what to say, her hand moving a piece of paper around on the table. "No, I just kept to myself…" She knew he wasn't the type to be too nosy into other people's business. "What about you?"

"Been busy with dive shop, Sofia's been a real help." He stopped watching Lily picking up her chopsticks, he could tell the small changes in her facial expressions. "I…" He stopped himself; he didn't even know why he brought Sofia up. "How did Mikey find you?"

"He came to my work, he was looking for information and I offered him a place to say." Lily's words so blunt, her eyes fixed on eating while she didn't want to talk about Michael.

The silence was tense, while they both ate, it was easy for Lincoln to understand why she didn't want to talk, and he always replayed their last conversation. He always thought of things he could have done differently that day, but it was too late to change anything.

Lily finished off her food, getting to her feet she walked into the kitchen, she exhaled trying to think of how she was going to get through this. It was hard to be in the same room with Lincoln. The guilt wasn't eating her as much as she thought it would, but with Sara alive, and Michael being happy, Lily knew that she really just was confused about her feelings.

Playing a hand over her stomach she found a glass going to pour herself a glass of water. Finding it hard to go back to the dining room, she jumped hearing glass smash.

Lincoln hearing the same noise jumped to his feet, he ran quickly into the kitchen grabbing Lily around her waist pulling her away from the big kitchen window. "Run!" He shouted watching her getting to an exit, it wasn't long before Sara and Michael were rushing out a bedroom and they were all fleeing the house.

Getting to a parking Garage out of breathe Lily leant against a wall, she noticed Sara in little, both of them bare footed.

"I can't believe they find us so fast?" Sara asked catching her breathe, she glanced to Lincoln, but then seeing how far away he was from Lily, and she didn't understand. "Should I call Bruce, get us someplace else, someplace safe?"

"No place is safe, They're not gonna stop, unless we stop them. Linc?" Michael started to head towards Lincoln, and Lily watched Michael using his serious face.

"You're thinking what I'm thinking?" Lincoln answered, and he felt like they really were going to have to call Donald Self now.

Michael took a cell phone from his pocket. "We're taking them down!" He dialled the number of Donald Self. After hearing him answer, he knew the other man was half asleep, so he cut to the chase. "We're in!"

Lily and Sara sat together, it was easier to have the men do all the talking, but Lily kept playing with her hands avoiding to look at Sara.

"Are you okay?" Sara's voice was soft, it made Lily's eyes shift to look at the woman's face. Sara and lily never really saw eye to eye, and as she studied over the woman Michael married to get his brother out of Fox River, she knew this woman couldn't be all bad.

Lily exhaled, "I'm just nervous, it's just…" She rolled her fingers together, "I'm meant to be away from all this, I left Lincoln to get away from this shit!" Her hands let go of each other as her hands covered her face in anger.

Sara exhaled, "Michael told me…" She paused. Lily looked up to Sara's face feeling sick, and she had no clue what Michael had told Sara. "That you three grew up together, that you was there for him and Lincoln when their mother passed away."

Lily felt some wash of relief, "Yes, we've been friends, practically family our whole lives." Lily turned to face Sara. "I know I've been a bitch, and I know it's hard for me to swallow my pride and admit I might have misjudged you."

"I think we both got off on the wrong foot," Sara added, she smiled holding a hand out. "Want to start again?" She asked looking from her hand to Lily.

Lily took Sara's hand shaking it lightly. "I'm Lily Carlin."

"Sara Tancredi…" She smiled brighter looking over the other woman. "I love your hair colour."

Lily glanced to her tips, and then laughed. "I like yours too." She noticed Sara still sporting the darker brown hair.

"So you really left Lincoln?" Sara asked looking to the door; she knew that they were going to be alone together for a while, well while Michael and Lincoln were arranging things.

Lily bit her lip, she now played with her hands again, "I wanted to leave Panama. After everything, I mean." She laughed. "I thought I saw your severed head in a box, and being held at gun point so many times I'd lost count. Being threatened with death…" She exhaled. "I just couldn't take it."

"I ran, and a part of me wished I found you guys. I just wanted…"

"To be free." Lily finished Sara's sentence, and she shrugged. "But Michael loves you, and I've known Michael long enough to know that he doesn't give his heart to just anyone."

"You know a lot about Michael…" Sara glanced back to the door. "I wished that I could know that much about him…"

"And in time you will…" Lily touched Sara's arm, and Sara flinched. "What did they do to you Sara?" Lily felt her eyes going over Sara's face. "Look, I know a battered woman when I see one."

"The company, they…" She closed her eyes trying to push the memory that haunted her away.

Lily took Sara's hand, for the first time she really was trying to be friendly. "Don't." Lily stated. "I spent weeks pushing everything my father did to me away, and I never told Linc or Michael about it, because I knew I had to face it alone." Her eyes looking into Sara's, she touched the other woman's face. "It will get better…"

"Okay ladies, you're gonna be staying in a motel." Donald said after opening the door. "Michael and Lincoln will be at a hospital getting Michael's tattoos removed." He then looked over Sara's face. "You'll be at a safe house until the plane ride to LA. I suggest you both get a good night's sleep, because tomorrow your work starts." He now nudged his head out the door for them to follow, and Sara and Lily got up, still holding hands as they were now lead out.

"This is it then." Sara said looking over Lily as they made their way to a van ready to take them away.

Lily squeezed onto Sara's hand, they both walked to the van before letting go of each other. "But what is the price of freedom?" Lily said before getting into the van, she didn't really know, but was hoping it didn't cost anymore life, or split any more blood.