Summary: An alternate ending to season 2. How things should have gone. MiSa

Disclaimer: I don't own Prison Break, just use it for fan fiction.

Chapter One

She paced around the small boat, eyes darting to the dock every minute. Fear was gnawing at her stomach. Where was he? Inwardly she cursed herself for falling for an inmate. It was her golden rule, the one thing she told herself not to do, and she broke it.

She absently picked up items and placed them back down, attempting a brief tidy inside the tiny cabin. She couldn't concentrate.

Suddenly her ears pricked. Was that his voice? Trying to remain calm, she exited the cabin and looked up, to be greeted by his face, the one that had been haunting her dreams since the day she first injected a needle into his arm. She lightly perched herself on the edge of the boat, and he stopped before her, hesitating to touch her.

"I got you message," she said, keeping her tone neutral. She studied his face, trying to depict how he was feeling. "Thank god I found you guys."

Before she could move, he reached down and pulled her into his arms, wrapping his around her and squeezing her tight. She drew in a deep breath, his warm scent filling her nostrils. At once, the stress and fear and worry pooled inside her evaporated, leaving her feeling weak. She was safe in his arms. In that moment, she knew that this was how she wanted to spend the rest of her life.

"Thank god is right," he spoke softly. Withdrawing slightly, he cupped her cheek with his palm and breathed in her sweet scent. She turned her face and laid a light kiss on his hand before straightening up.

"Michael, Lincoln's free," she said, and he stiffened slightly in surprise.

"What?" came a voice from behind her, and she turned to see Lincoln, a shocked look upon his face. She was so focused on Michael she had barely noticed him. A smile spread across her face.

"It's all over the news. Paul Kellerman came forward, he had all the documents and he made a full confession."

Lincoln simply gaped at her, speechless.

"Are you serious?" Michael spoke up, hardly believing what she was saying. Was all the time and effort from the plotting, the escape, the running, about to pay off?

"Yeah," she replied, turning to look at him again. Assure herself he was there with her.

"Everything?" Lincoln asked; eyes still wide.

"Everything. All charges," she confirmed.

Lincoln felt his knees weaken, and lowered himself to a small seat. A million different emotions were running through him, and he took a few deep breaths to get his mind wrapped around the fact that he was now a free man. He was free. No more hiding. "What about Michael?"

Sara smiled slightly and turned back around to Michael. "Uh, a friend of my father's getting into it, but he's pretty confident that under the circumstances no one's going to pursue you on this." She reached a hand up to him and lightly stroked his chest. Michael said nothing, gazing into her eyes then glancing down. This seemed too easy. Was it really happening? He brought his hand up to her shoulder to make sure she was truly there; his mind wasn't playing tricks on him.

"I need a drink," said Lincoln, breaking the silence. Sara gave a slight chuckle, and moved to get up.

"I'll see what I can find," she told him. As she rose to her feet, Michael squeezed her shoulder and she brought her hand up to cover his for a moment. Then she disappeared to the front of the boat and down to the lower deck, leaving the two brothers together. Michael sunk down to the side of the boat, attempting to gather his thoughts.

Lincoln got up and moved into the cabin, placing the gun on the table and picking up a paper clip. Moving back outside, he stood in front of his brother and gave him the clip. "Help me out of this?" he asked, holding out his handcuffed wrist.

Michael swiftly picked the lock and the cuff fell to the floor, yet he hardly took any notice. "We did it, Linc. We did it."

"No," a new voice interrupted them. The two brothers snapped their heads up, to find themselves face to face with a gun. "You almost did it." It was Kim.

Lincoln fired up at once. "You want the money?" He grabbed the pack, containing their financial future, and flung it at the man. It rolled on the dock and stopped before his feet. "Take the money. Take it."

"You think this is about the money?" Kim sneered, kicking the pack off the dock. Michael watched the bag hit the water and begin to float under the dock.

"Then what is it about?" Michael asked firmly, trying to keep a hold on his emotions. "My brother's been exonerated. The president stepped down. We're not a threat any more. It's over."

"You may be done with us, but that doesn't mean we're done with you. The police are on their way." He kept the gun trained on Lincoln.

"It started with me," Lincoln said harshly, eyes shooting daggers at the man. "Let my brother go."

The man shook his head slightly. "Oh, that's sweet. That's sweet. You don't hear that much anymore, that sort of fidelity between families. Two brothers that will go to the end of the earth for each other." He turned slightly and aimed the gun at Michael. "Too bad only one of you survive." He turned back quickly to Lincoln.

"Don't!" Michael yelled, but the sound of a gunshot rang out, scaring the birds out of the trees. Yet it took him less than a second to realise what had happened. The man still held the gun out, but did not move. A dark red patch was steadily growing on his chest.

As the faint sounds of sirens began to be heard, Michael spun around and saw Sara crouched at the top of the boat, a gun in her hand. Panic was etched across her face, and he could see her shaking over what she had just done. Quickly, he jumped into action, knowing they only had moments.

"Start the boat NOW!" he shouted at Lincoln, who was standing in shock trying to process the event that had just taken place. The yell managed to snap him out of it, and he jumped to the controls and began the engine. The boat roared to life

As Lincoln was doing this, Michael dove into the water. Before Lincoln realised what was happening, Michael had grabbed the pack from under the dock and pulled himself to the side of the boat. Lincoln hurried over and extended a hand to his brother, who ignored it.

"Move now. Get us gone before we're dead," he barked, heaving himself into the boat. Lincoln compiled, and the boat jerked to movement. The sound of the sirens increased, deafening them.

Michael glanced back at the receding shoreline, and saw officers jumping out of the squad cars. He saw the glint of guns in their holsters, which snapped a thought to his mind. Sara!

He spun around, and saw her still crouched with the gun in her hand, shaking. A silent tear trailed down her cheek. She could feel his eyes on her, yet did not look up at him. She had just killed a man. She took a life. She had spent her whole career saving people's lives; she wasn't supposed to take one.

Without warning, a gunshot was heard and a bullet ricocheted off the metal railing, barely a foot next to Michael. He dove over to Sara and grabbed her arm, pulling her out of view of the police. Another bullet flew past, barely missing them.

"C'mon Linc, we need to get out of here NOW!" he yelled. Lincoln pushed the throttle right down and the boat shot forward, startling Michael and Sara. He wrapped an arm around her waist and pulled her close, steadying her. She let out a dry sob, and buried her face in his sweater. She was still clutching the gun, and he eased it out of her hand and shoved it in the pocket of his jeans. With her hands now free, she wrapped both arms around him and held on tight, as if she would die if they lost contact. He was still dripping wet from retrieving the money, but she didn't even seem to notice.

"Michael! Where are we going?" Lincoln's voice rang out. Michael bent slightly and picked Sara up, wrapping her legs around his waist for support. He carried her into the small cabin, where Lincoln stood at the helm steering. He gently set her down on the couch and crouched down in front of her, but held onto her hands. She kept her face down, but he could see the shining trail of tears making their way down her cheeks. She was still trembling. He reached up and cupped her face, forcing her to look up. As he stared into her eyes, he softly brushed the salty tears off her cheeks with his thumb.

"Michael, I took a man's life," she whispered, her voice cracking.

"It's okay. Don't think about that now, its okay. I'm going to take care of everything. I won't let anything happen to you," he told her softly. He leaned forward and pulled her into another hug, one hand coming up to stroke her hair. She melted into his touch, and slowly brought her arms around his neck, pressing them tighter together. They were together, and she was complete, and she wanted him to know.

"I love you Michael," she said quietly, barely above a whisper. She felt his grip on her tense up, and internally she froze. Oh god, what if he didn't feel the same? What if she ruined this? She couldn't survive without him, she knew this, and she couldn't lose him now. Not now, not ever.

Michael, on the other hand, could hardly believe what he had just heard. She told him she loved him. After all he had put her through, after all he had done, and she still wanted him. She loved him. "I love you too Sara," he told her just as softly, moving his head so their foreheads lightly rested together. He gazed into her eyes, and saw both love for him, and uncertainty. "I love you," he repeated, and leaned forward slightly. Their lips met, and through this one kiss they each showed the other how much they meant. They were soul mates. No matter what, they would go on together, forever.

Lincoln watched the two, a small smile upon his face. His little brother was finally getting what he deserved. Michael had spent his whole life looking out for everyone, putting them first, and missing out on a lot because of this. He was finally getting his chance, and Linc couldn't be happier. His mind began to drift over to Veronica, but shook his head before emotion could overcome him.

Michael and Sara slowly pulled apart, and Lincoln nervously cleared his throat. He didn't want to break up such a tender moment, but he knew that there were police after them, probably on boats hunting for them by now, and he needed to know what to do.

"Uh, Mike? Sorry, but I'm driving blind here. And the cops know we're on the water…" he began, feeling guilty for interrupting. Michael and Sara both glanced up, remembering where they were and what was happening. Michael stood up quickly, and rummaged around for a map. Sara toyed with the ring on her finger, a red tinge evident on her cheeks.

Michael found the map he was after, and spread it out in front of Lincoln. "We're here, heading this way. If the police have gotten on the water, they'll be coming from here," he said, pointing at various places on the map as he spoke. Then he pointed to a small device on the dash. "This is a tracker, it will tell us of any boat within 500 yards of us. It also blocks our signal so we can't be seen. There is a cabin 300 miles away, it will take us about two or three days to get there. We'll be safe there. We can stay til things die down. You're a free man now, Linc, but the cops are still after me, and now Sara. We have to hide out until it is all straightened out."

Lincoln couldn't help but admire how systematically and methodically Michael had planned the entire escape. He had backup plans for backup plans, every little detail worked out for anything that could go wrong. How he appreciated it.

"So, uh, we'll be on the water for the next three days," Lincoln remarked. "Guess I better get comfortable." He sat himself down at the helm and picked up a nearby magazine. He caught Michael's eye, and gave a slight nod to Sara, who was still staring at her hands, and a subtle wink. He then turned his attention to the magazine.

Michael gave a small sigh of relief; Lincoln could be pretty attentive and considerate at times. He bent back down to face Sara, and covered her small hands with his. She looked up into his eyes, and found herself caught in his deep gaze. If felt as if he was reading her soul. To a point, he was. Michael stared into her beautiful brown orbs and saw so many emotions. What made him worried was seeing the pain, fear and apprehension in her eyes.

"C'mon," he muttered softly, and stood up, pulling her along with him. She allowed him to guide her out of the tiny cabin, and around down to the lower deck. The room was small, just a double bed, a small chest of drawers, a bench with a couple kitchen appliances, and a tiny bathroom. The air seemed slightly thick, as if there was a layer of tension covering them. She couldn't stand it

"Let's get you out of these wet clothes," she said, tossing him a towel. His eyes never leaving her face, he peeled of the wet sweater, and the shirt underneath. Sara glanced at his chest, blushed slightly, and then took the wet items from his hand. "There are dry clothes in the drawer," she told him, and exited the room to go to the deck outside, giving him privacy to get changed.

Michael was surprised; he had gotten the boy to stock the boat with certain items, but hadn't thought of clothes. Pulling the top drawer open, he saw a couple pairs of pants and tops that would be Sara's. The next drawer down had several pairs of jeans and shirts. She must have thought ahead and brought them with her. He smiled, and grabbed a pair of jeans and a loose shirt. He hurriedly towelled himself off and put the fresh clothes on, not wanting to leave her alone any longer.

Michael walked out onto the deck, and saw Sara sitting on the side of the boat, gazing into the water. It pained him to see such a troubled look upon her face, yet he knew that she was dealing with so much right now. In just weeks, she had aided in a prison escape, had a drug overdose, been almost tortured to death, gone on the run, and killed a man. He wished he could take away all the pain. The best he could offer her though was an outlet.

"Sara…before, on the dock," he started as he took a seat next to her, but she cut him off.

"Don't tell me its okay Michael, because it's not. I killed a man Michael. I shot and killed him. I've spent my life saving lives, yet I've just taken one. It's not okay," she said vehemently. Her eyes started to shine, and she took a deep breath to calm her emotions.

"That man was going to kill Linc," he replied gently. "Then he would have shot me, and probably you. If it hadn't been for you, we would be dead right now. I'm not saying that everything's okay; I can only imagine what you're going through. But I just want you to concentrate on the fact that you saved three lives today. You saved us. You need to understand that to accept what happened."

The tears in Sara's eyes began to spill over. In one swift movement, Michael reached over and pulled her close to him, wrapping his arms around her in comfort. Sara began to sob, clutching his shirt which was slowly dampening with her tears. She was not only letting go of her feelings from the event on the dock, but also the stress and pain from the previous weeks. She felt like a dam had burst inside her, and the tears kept coming. She kept her face buried in his shoulder, hands clutching at his chest. He murmured soft words of comfort into her ear, whilst rubbing soft circles on her back.

They remained like that for quite some time, until her tears dried out and she stopped shaking. Moving two fingers under her chin and tipping her heap upwards, he gazed down at her red, tear streaked face. He softly kissed away the salty trails on her cheeks, and wiped a stray tear with the pad of his thumb. Gently, he traced the outline of her lips, and planted a feather light kiss upon them.

"Sara," he said slowly, his voice cracking on the last syllable. She glanced at him, a serious expression upon her face, and he reached across between the two of them. Picking up one of her hands in both of his and giving it a small squeeze, he drew in a deep breath.

"So much has happened in the past few weeks. Its' been so quick, and we've been together and apart constantly. I haven't had a chance to talk to you properly, without interruptions. This isn't how I wanted things to turn out," he began.

"Michael, I don't," she broke in but he brought his other hand up to her cheek, stopping her.

"Please let me get this out first, I need to tell you this," he said softly, tracing her cheekbone with his finger. The light touch sent chills up and down her spine.

"In the beginning, when I got into Fox River, the female doctor was part of my plan. You weren't. I wasn't supposed to fall in love with you, I was meant to play the part but it became too real. Right from that first needle you gave me, I felt something, and it has grown ever since. I need you to know that everything I did with you was real, not just part of a plan. The origami flower, the kiss – I meant it all. Yet I asked you to leave the door open. I used you, and I hate myself for it. My actions hurt you so much, and because of me you hurt yourself. Now you're on the run from the police, stuck on a boat. Your live has completely changed because of me, and I am so sorry, I never meant to drag you into it like this."

At this point, Sara couldn't listen to any more. She leaned over and brushed her lips against his, silencing him. She gazed into his eyes.

"Don't say another word," she told him gently. "I don't want to hear you apologize. You had to do what you did, to save your brother, and you have. I left that door open out of my own free will, I had choices and I made the decision to stick with you. Yeah, my life has changed, but right now I feel so lucky to have you in my life. If you didn't do what you did, we wouldn't be together, and that thought hurts more than what I've experienced in the past few weeks. I love you."

"God, I love you so much," he whispered, running his hands through her hair. She closed her eyes at the gentle touch, and a small yawn escaped her lips.

"Tired, are we?" he smiled; glad to ease the heavy emotion in the air. She let out a small chuckle.

"Being on the run does that to you. Why, Mr. Scofield, are you feeling a bit sleepy too?" she teased him, just as glad to lighten the mood.

"Well actually, a nap couldn't hurt either of us," he replied. He stood and extended a hand to her with a slight bow, which she smiled at and accepted. He led her back down to the lower cabin, and as he lay down he pulled her along so she fell next to him. Nerves took over her straight away, despite all she had been through with this man over the past weeks, despite their declarations of love, she still felt slightly embarrassed to be lying on a bed with him in such a small room. Being the attentive person that he was, Michael picked up on this and thoughtfully didn't try to embarrass her further. He simply lay back on the bed and closed his eyes, drawing in a deep breath and slowly releasing it. He felt the mattress sink lightly next to his torso, and he stole a peek to see her laying next to him, about a foot in between them. She had her eyes closed, and he used the moment to study her face – the way her soft brown hair fanned out around her face, her soft lips, her long lashes.

"Like the view?" she said suddenly, opening her eyes and rolling her head to look at him. To be completely honest, she felt somewhat flattered to catch him staring at her.

"How did you know I was looking?" he asked with a guilty smile, avoiding answering the question.

"Give me some credit; your eyes were burning a hole in my face." She smirked, and reached her hand out to his face. Lightly skimming his cheekbone with her finger, traced down to his collar bone, and then rested her hand upon his chest. His eyes never left hers the whole time. Slowly, he shifted closer until they were just touching, and he leaned over and placed a chaste kiss upon her lips. He began to pull away, but she tightened her grip on his chest and leaned in, giving him a deeper kiss. He returned it, and they remained like that for a few moments, until she pulled away and rested her head on his chest. He kissed the top on her head and brought his arm around her shoulders.

They both closed their eyes, and Sara allowed herself to finally relax in his arms. His hold was warm, comforting, but most importantly – safe. She was almost asleep, when she heard him murmur something into her ear.

"I loved the view."

TBC…what do you think?