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Alias Fanfiction

Waiting (Part III)
By Rebecca

Summary: This story takes place during Sydney's missing two years and it is from Will's point of view in the witness protection program.
Rating: So far G-PG, it might go up to PG-13, but it will be a mild PG-13.
Spoilers: Anyone who has not finished Season 2 should not read this.
Disclaimer: I do not own any of the characters, except the small ones, like Will's friends. I am not making a profit off this story, I am writing it to show my two loves, Alias and writing. If you feel I am overstepping any copyright guidelines, please let me know.

. . .

It was almost two weeks after that Friday when Will returned to his apartment after work. He sighed, sat down on the couch and had just finished his second beer when the phone rang. The harsh ringing startled him and he jumped, then almost tripped over a table trying to answer it.

"Hel-," Will's voice was scratchy, he cleared his throat and tried again, "Hello."

"Jonah?" asked a peppy, female voice on the other end.

"Yeah." Will knew he didn't sound that intelligent, and didn't care.

"Hey, it's Naomi."

"Hello Naomi." Will tried to add a note of happiness to his voice. Naomi was a woman who lived across the hall from him, tall, blond and friendly. Matt encouraged Will to date her whenever possible, and, though Will couldn't envision himself dating her, he made a conscientious effort to be friendly whenever he talked to her.

"You need to give your cousin better directions." Her voice had a slightly teasing note to it.

"Excuse me?" Maybe it was the alcohol, but she made no sense, "My cousin?"

Will heard Naomi half-cover the mouthpiece and whisper to some on the other end, "What's your name?" she gave a girlish laugh, "Sorry." Will wasn't sure if she was apologizing to him or his...his cousin. "Your cousin, Eric Weiss, you sent him to my apartment."

Will froze and for a moment he forgot where he was. This must be bad, why was Agent Weiss, a man Will hadn't seen since his de-brief almost two years ago here, instead of his case officer.


Will swallowed, "Yeah, I'm here."

"I was just going to send your cousin down, I just didn't know if you were going to be there."

"Fine, thanks."

Will barely had time to hang up the phone, before he heard a knock on his door, Will opened it warily and Eric Weiss, a large man almost six inches taller than Will, and a good deal wider, enveloped him in a bear hug.

"Jonah, great to see you buddy."

"What are you doing here?" Will asked, "Where's Bill?"

"Your case officer was wounded, gunshot, he asked me to come in his place. He sent direction through one of the interns."

Will laughed, "If I were you I'd find out which one."

Weiss laughed too, "Already being done."

Will offered him a beer, took another one for himself and Will offered Weiss a chair, before sitting on the couch. Will went through the motions he did every time with his case officer. After they had finished, Weiss sat back and took a long sip of beer.

"You looked good," Will said.

"Thanks," Weiss sighed and shook his head, "It's all Mike's fault, he is convinced that I can't get a girlfriend without losing weight. It's like ever since he got married he has this need to match all his friends like ducks." Weiss moaned, "It's enough to drive any man to drink."

Will was still focused on what Weiss had said before, "Michael Vaughn is married? When did this happen?"

Weiss looked guilty, "I shouldn't have said anything-"

"Off the books."

Weiss sighed, "Mike has been married for almost three months now."

Three months, "To who?"

Weiss sighed again, uncomfortable with the questions, "Her name is Lauren."

"And?" Will's brain felt like it was digging through mud.

"She's NSC, her father's the senator of Virginia-"

"Is she pretty?"

Weiss threw up his hands, "Hell if I know!"

Will was almost talking to himself, "I always thought he loved Sydney, I thought-"

"Sydney's dead, Will."

The harshness of the words hurt, Sydney's dead, and the man that harbored the place in Sydney's heart that Will always wanted was married. But Will saw another emotion in Weiss's voice, he didn't like Vaughn's wife and he thought that Vaughn had given up too easily.

"What do you think of her?" The softness of his voice surprised him.

Weiss sighed and rubbed one hand over his eyes, "Hell if I know."

Both men finished their beers in silence.

. . .

The next day at work Will couldn't concentrate, he came close to walking off the fourth floor of a building, and he hit his thumb with his hammer twice. After the second time, Matt grabbed him by the shirt and pulled him over, annoyed.

"What the hell is your problem, Jo?"

"Nothing." Will pulled out of Matt's grasp.

"You aren't drunk, are you?" Matt looked closely at Will.


"Then what is wrong?"

Will looked away, almost fighting back tears.

"Hey, man," Matt's voice was soft, "It's me, what is wrong?"

"He got married." The anger in Will's voice surprised him.


"Syd's husband."

"The girl you-"

Will nodded, disgusted, "He dropped her, forgot about her, lost faith, just took up with the first..." Will had to restrain from saying something that was less than kind about Vaughn's wife. Will knew he was being unfair, but he was so frustrated he couldn't help himself.

"What's that jerk's name?"

Will shook his head, angrily, "Michael."

The two friends stood in silence for a moment, then Will laughed, "I'll just pretend that every nail I hit is Michael's face."

It was the end of the day, and Will had already packed up and gone home. It was Matt who was left standing behind, watching the fiery sun crash behind the tall skyscrapers. Michael was married. To Matt Hoffman, Michael was a name without a face, just another person dredged from the memories of friends. But to Jeff Balt, Michael could only mean one person, Michael Vaughn. Jeff and Michael were friends who were recruited for the CIA the same year and underwent training together. They had saved each other more times than they could count or remember. They were even partners for awhile, but then almost four, no it would be about five now, years ago. Then Jeff had begun working with the Witness Protection Program, Michael became focused on the Alliance. After Jeff was transferred to D.C, they promised to keep in touch, but, as it turns out, it is hard for spies to commit anything to paper. When Jeff heard the Alliance had been defeated, he immediately flew out to L.A. to see Michael. That was when he first met Sydney Bristow. God she was beautiful and Michael was so in love with her and she with him. He spent a week with them, touring L.A., catching up with Michael, Eric and other friends that he hadn't seen or spoken to in years.


Jeff stretched as he walked down the long corridor from the plane, he searched the crowds for Michael and jumped when he felt a friendly slap on his back.

"Jeff! With the storms raging across the Midwest, we thought that you would be trapped somewhere south of Chicago."

Jeff turned to face Michael, and enveloped his friend in a hug. Though his friend had more lines around his eyes, Michael looked happy. Jeff turned his attention to the beautiful woman standing slightly to the side of him. She was very tall, almost as tall as Michael and had long, brown hair and deep brown eyes. She extended and delicate hand to shake, but Jeff didn't miss the strongly defined muscles in her arms, this girl could be a boxer!

"Sydney Bristow." Her smile was genuine, without a scrap of fakeness in it.

"Jeff Balt," he smiled back.

Jeff handed a bottle of wine he had been carrying on the plane to Michael, unsure of how to present his gift. Michael, seeing his discomfort, nodded, saying, "Syd's part of us, Jeff."

That explained the muscles.

"Then this goes to both of you, congratulations."

"Thank you." Sydney and Michael spoke at the same, causing all three of them to laugh.

"Sydney's the reason the Alliance is gone, Jeff, she's amazing."

Sydney blushed, "Vaughn..." He kissed her softly and they left for the terminal to get Jeff's bags.

***End Flashback***

He left L.A., sure that the next time he returned would be for the wedding of Michael Vaughn and Sydney Bristow, but it wasn't, he returned for Sydney's funeral.Jeff should have guessed that the Sydney Jonah was in love with was the same Sydney. The WPP gave him few details on Jonah's background, he was a close friend of a CIA officer who was killed, an enemy agent stabbed him, he needed to disappear. "Watch him, protect him.", were the only directions given. With the connections that his brain was making, Jeff remembered vaguely, a picture in Sydney's apartment where they had stopped for beer, a picture of none other than Jonah. Reaching into his coat pocket, he pulled out his cell phone. He dialed a number, relayed his agent number and was connected to the office of Agent Weiss.

"Weiss." Came the voice over the other end.

"This is Jeff."

"Hello." Weiss's voice was guarded now, mentally revisiting all the reasons that a friend he hadn't spoken to in over two years was suddenly calling him.

"He's married?"

Jeff heard Weiss sigh, "Yeah."

"What's her name?"

"Lauren Reed."

"Any relation to the Senator?"

"His daughter."

Their conversation was stilted and Weiss blamed Vaughn, Vaughn who was making him lie to all his friends. Vaughn who was forcing Weiss to put on a happy front about a marriage that was doomed from the start.

"When was the old boy planning on telling me?"

"You were in deep cover."

They talked for a couple more minutes, stepping around the issue they both needed to talk about. An issue that was about as easy to avoid as an elephant. They said good-bye, hung up and Jeff tried to become Matt Hoffman again, but slipping back into character wasn't as easy tonight as it usually was. Because it didn't just feel like Michael had betrayed Sydney, it felt like Michael had betrayed him.

. . .

Matt was moody for the next few days, Will noticed, depressed and angry. When Will tried to talk about it, Matt brushed him off. Part of Will was annoyed that Matt didn't trust him. After all, Will confided in Matt on everything, well everything that he was legally allowed to say. But part of Will barely noticed, that part was still caught up in the past, and the words that Weiss said that wrenched Will's heart. Michael Vaughn was married.

The three months that passed after Will learned Vaughn was married were no different than the past two years of his life had been. He went to work, made small talk with Matt, Neal and his other friends, went home and got drunk. These were his favorite moments, not the drinking, but how the alcohol allowed him to reach back for his memories of Sydney. It was one of those Friday afternoons, and Will was packing up to go home when he saw a reflection in the a large mirror that was hanging in front of him, slightly to the side. Not just any reflection, but her reflection, Sydney's. Will spun around with a cry, but no one was there. Breathing heavily, Will knelt next to his bag and took out the gun he kept in a hidden pocket, he quickly assembled it and slipped it in a more accessible pocket. If Sloane thought he could get Will this time, he hoped that his assassin was in for a surprise.


It was her voice, beautiful and sweet and lovely, Will rose slowly, turned around and saw, Sydney. Even in the oversized lumber jacket and jeans, it was undoubtedly her.

"You're dead." It was the first words out of his mouth, the only words running through his head.

Sydney gave a watery laugh, then looked around at the construction site, "I want to tell you everything, is there some place we can talk?"

Will was calm, "Sure, let me get my stuff." Will walked over to his bag and let is hand feel the harsh metal of the gun, ideas running wild in his brain. Sydney Bristow was dead, this woman, whoever she was, must be a double, like A.G. Doran. For all his pretending, Will knew that this woman was not who she claimed to be, and if Sloane thought he could trick him again... Will spun around, pointing the gun straight at her heart, "Hands up."

Sydney dropped to her knees hands in the air, "Will? What the hell are you doing."

Will felt anger boil up inside of him, "Sydney Bristow died, two years ago. I know about Project Helix, I know what you are."

"I'm not a double, Will, I swear I'm me."

Will took his phone out of his pocket and punched in a number, "I'm calling Langley, telling them you're here."

Panic rose up in Sydney's face, "Will, please you can't do that. I'm a fugitive, if you make that call, you'll burn me."

Anger made Will sharp, "That's convenient."

Sydney was crying now, "When we thought you were the second double, you told me to ask you something, something only you would know. Ask me something only Sydney would know, ask me something obscure..."

Will pocketed the phone, still leveling the gun, "When I had my interview for the newspaper, something happened to me that day, what was it?"

Sydney was practically screaming, "Someone bumped into you on the elevator, they spilled coffee on your new white shirt. You were freaked, but the editor said it made you look like a working reporter, she gave you the job."

Will couldn't think, he couldn't breathe, this was Sydney, his Sydney, "Oh my God."

Sydney stood up and hugged him hard, "You're my best friend, my oldest friend."

Will hugged Sydney back with all is might, as his tears ran down onto her head.

***Note: In my story all the stuff from "Remnants" has happened and Will and Sydney have returned to Will's apartment. ***

Will helped Sydney carry her bags up the three floors to Will's apartment, since the elevator was broken again. Once upstairs, they collapsed on the floor in front of Will's bed, and Will got out two beers, more out of habit than thirst, but he didn't touch his and noticed Sydney didn't either. They had already been through four beers each when they had gone to a restaurant, in the back corner and Sydney had told him her entire, crazy story. Even after all he had seen as an analyst, Will couldn't wrap his head around it.

"Vaughn's married." It was an out-of-the-blue comment.

"I know." Will replied, then mentally kicked himself for it. Sydney looked at him curiously, but didn't press.

"Have you met his wife?"

"Lauren? Yeah, she's..." Sydney shrugged helplessly.

"I know."

Impulsively, Will came over to Sydney and gave her a big hug, wrapping her in his arms. Sydney began to softly cry and Will held her and rocked her.Sydney sobbed, "I shouldn't hate her, I know I shouldn't but...but I just can't let go...I"

"Shhh, baby." Will hugged her tight, letting her angry tears pour down her face. Suddenly, Will felt her kissing his neck, then up until her soft lips met his. Although Will knew he shouldn't be doing this, he couldn't stop kissing Sydney. Before he knew what was happening, Sydney had her hands under his shirt, beginning to lift it off.

"Syd..." She continued to kiss him, Will pulled back from her, "Syd...we...I...we're both so..." But she continued to kiss him and Will removed her shirt, and they fell back onto his bed, Will kissing her with as much passion as she was kissing him.

. . .

It was still the early hours of the morning, between five and six, if Will had to guess from the meek sunlight streaming through the curtains. Sydney was asleep, her peaceful face on top of his arm, her breath steady. Will resisted the urge to trace her delicate features with his finger. She looked the same, but different in many ways. Her hair was longer and lighter, as if it had been dyed a long time ago. Her eyes were sad and slightly puffy, the eyes of someone who cried to much. Worry and pain had given creases around her eyes, and fine lines radiating out from the corners of her mouth. She had the look of someone who had aged before their time and it made Will sad. Sydney stirred suddenly, surprised to see Will, as if she had been expecting someone else, Will knew who and it hurt.

"Hey." Her voice was light, still tainted by sleep.

"Hey." Will did run his finger down her face know, and kissed her forehead. From the bedside table Sydney's phone rang, startling them both. Sydney rolled over and picked it up.

"Hello?" She paused and her voice took on a strained tone, "Yeah I will, thanks."

"Who was that?"

Sydney gave Will a trapped look, and he knew she couldn't answer, "Never mind." Will smiled and kissed her again. Sydney got up and dressed quickly, Will watched her with some regret.

"I have to go."

"No you don't."


"I'm serious, Syd. Stay here, with me, you don't have to go back to that life to..." Vaughn's unspoken name hung in the air.

"Will," Sydney say on the bed, serious, "I'm sorry, but I can't, it wouldn't be fair to either of us. Being with you, but I'm still in love..."

It hurt and Will turned away.

"Will?" Her voice was watery and broken. "I love you so much, and you are my best friend, but..."

Will smiled at her, "I know Sydney, I know."

Sydney smiled and swallowed her tears, "Is there anyone...?"

"A painter, lives in this building, Matt has been trying to get me to ask her out."

"You should."

"So should you, Syd. We both need to get on with our lives, and I can't if you don't."

"I'll try."

"Me too."

They laughed and hugged again. Then Sydney gathered her bags and left.

Will spent the rest of the day in his apartment, he didn't go to work, he ignored his phone. He just thought about her, every hug, every kiss, the brief moments of passion they had shared last night. Then late in the after noon, Will went to his refrigerator to get his daily beer. Then, out of the corner of his eye, he saw the phone. Will picked it up and went to the window and looked out, to where the sun was just beginning to set.For a long time he just stood there and thought. He remembered the first time he saw Sydney for who she was, in that club in Paris, three? four? years ago. How that revelation had changed his world. Still, even after everything he had been through, tortured, arrested, stabbed, and the numerous times he had been almost killed. He wouldn't give it up for anything though, to know Sydney, nothing else mattered. He would be lying if he said it didn't hurt, if he wouldn't still think of her with a mixture of hurt and longing. But Sydney had moved on, not moved on because she had never really been...his. The apartment grew dark and Will still stood there, then the hint of a smile began to play around the corners of his mouth.

"I can do this," he thought, "I can love Sydney, but not have her memories destroy my life. I can do it."

"I can." This part he said aloud, and dialed a number on the phone.

"Hello?" It was Naomi, her peppy friendly voice, that answered.

"Hey Naomi, this is Jonah." Will smiled and when he said the next words, he felt free for the first time since Sydney's death, as if he was floating above the clouds.

"Jonah?" He realized he was still on the phone.

"Do you have any plans for Saturday?"

The End

. . .


Please tell me what you think of my story and if I should continue. Any input, good or bad would be greatly appreciated.

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