Sometimes the Truth is Best Kept Hidden

This is my first alias fic so cut me some slack. The whole thing with Francie's double never happened and Francie is still alive. Will was never placed in witness protection and he still is in L.A. and he works for the CIA as an analyst. Syd and Francie are still living together in their old apartment. Sark, and Derevko are still alive. Emily and Diana are also still alive. My version of season 5 and Syd and Vaughn are engaged. Syd/Vaughn Weiss/Nadia Will/Francie.

I do not own Alias. If I did, this is how the show would have turned out.

Chapter 1- The FAINTest idea

The apartment:

"I'm back", Sydney yelled as she walked through her apartment door, dropping her bag. Her mission had been a complete success. She went to London to get a disk the CIA wanted to keep away from Sark. No one knows what the disk is for, but Sydney was not going to stress about that tonight.

"Hey Syd, how was your trip?", Francie inquired from the kitchen.

"The client was one of the most annoying people that I have ever met and am so glad that I am home", Sydney said as she collapsed on the couch.

"Well that is good because I was thinking and I think that we should have a day at the spa", Francie said as she rounded the corner and sat next to Sydney.

"We should, it has been so long, how about this weekend? Can you get the time off from the restaurant?" Sydney's cell goes off. She gives Francie an apologetic look and picks up the phone.

"Hello"

"Hey Syd, Sloane wants a debrief ASAP" Vaughn said

"Ok, I will be right there". "There is a problem with the client that I was just telling you about so I have to go in, but I totally agree on the spa. I'll see you later Fran".

"Ok, bye Syd".

APO:

As Sydney entered APO she got this feeling that everything was going to work out. She spotted Vaughn and rushed over to him and asked him what the emergency was.

"Syd they figured out what the disc was for and we have debrief in two minutes". Vaughn put his hand on the small of her back and led her to the conference room. It was still so amazing how something that simple made Sydney so happy. As she sat down she noticed that something was going on between Nadia and Weiss and made a mental note to ask Vaughn about that later. Sloane walks in and Sydney starts feeling the hate boil inside her. Vaughn notices this and takes a hold of Sydney's hand and squeezes it gently to let her know that he is there for her.

"Thanks to Sydney we have acquired a disk that gives us the access points to get to a blackmail disk. For those of you who remember from SD-6, Derevko had a blackmail disk. This one is similar but much bigger and more in-depth. The disk belonged to this man, Alehandro Salviskio. (A picture of the man comes up on the many screens in the room.) He is former KGB and K-directorate. Recently he became freelancer and became very suspicious, which is why he made the disk to keep his associates from betraying him and his enemies on high alert. He was found dead a couple of days ago in an apartment in Venice. The blackmail disk was rumored to have been given to his second in command and his brother, Jervano Salviskio. Sydney, Vaughn you are going to Prague. You are going to a party to celebrate the engagement of Lilly and Ramundo Salviskio. You will be going in as a married couple, Monique and Jerome Tollures. The disk is in the study behind a copy of a Renaissance painting. Vaughn and Sydney on point, Dixon on back up, and Weiss and Nadia will be on coms here. The mission details will be on the plane, Marshall will go over Op-tech, wheels up in three hours".

At this everyone left the room and Vaughn and Sydney walked over to Marshall's office with Vaughn's arm around Sydney.

The apartment:

Syd walked through the door to find a surprise. "Oh my god, I am so sorry, oh my…"

"Hey Syd, you came back earlier then expected", Francie said as she fixed her shirt and hair. Will was turning three shades of red and Sydney had to try so hard not to laugh.

"Ummm, Francie I will call you later, bye Syd", Will said as he raced out the door.

"Fran I am so sorry and second I need details, but the bank is sending me back to London to meet with the client and see if I can fix the problems and his anxieties about the bank. I might end up strangling the guy, but I will be back for our weekend. Make the reservations and be prepared to be grilled about you and Will".

"Syd, the bank is sending you on another trip, why can't someone else go?" Francie said as she walked towards Syd's room to help her pack.

"Well, because I am the one that was sent before and they want to have the client less freak out, and they think that that will happen if he deals with the same person. Also, don't try and change the subject, I will not forget while I am gone and there is no way that you will able to get out of my interrogation." At that they both laughed.

"Interrogation, you sound so official. But have a safe trip."

The airplane:

"So when I went home, I found Will and Francie making out. I was completely shocked." Sydney said as she laced her fingers with Vaughn.

"Wait Will, as in the Will that I know and Francie, as in the person that you are living with Francie?" Vaughn asked, just as stunned as Sydney was.

"Yeah, and what is up with Nadia and Weiss? I see some sparks flying!" Sydney said as she leaned further back in the leather chair of the CIA issued plane.

"Weiss is asking her out tonight and he had me help him plan it." The plane starts to shake and Sydney gets a little nervous. Vaughn senses this and starts rubbing her back in slow circles.

"Are you ok sweetie?"

"Yah, I just get a little nervous when the plane shakes". The plane starts shaking violently and the captain tells them too buckle in their seatbelts. Vaughn sees that Sydney is on the verge of tears and pulls her in for a tight hug and kisses her forehead in attempt to calm her nerves. Vaughn understands her worries. On a couple of missions ago, her plane was having some malfunctions and had to do an emergency landing. He was on the phone with her the whole time and at that moment, when he thought that he could lose her again, he decided that he was going to ask her to marry him. And Voila, that is how that got to be at the present.

"I am sorry Agents, but we are going to have to have an emergency landing. There seems to be a storm coming and we have been ordered to land in Paris". Vaughn goes up front to talk to the pilots and Sydney starts feeling queezy and all of the color drain from her face. When Vaughn comes back, Sydney is passed out on the carpeted floor.

"Sydney…SYDNEY". At Vaughn's screams, Dixon comes running over. He tells the pilots to have a ride to the hospital for Agent Bristow.

Dixon comes back to find Vaughn cradling Sydney's head in his lap. He is stroking her chocolate brown hair and Dixon once again sees their love. Dixon then starts worrying about his own wife and kids and almost envying the way that Syd and Vaughn are able to stay so truthful. The captain makes his final announcement about descent and that the ambulance is at the airfield.

Once the plane lands, Sydney is rushed into the ambulance.

"I am sorry sir, but you are not allowed to come with us".

"Like hell I am not, she is my fiancée", Vaughn yells.

"I am sorry sir, I did not know. The other car is for your friend". Dixon gets in the car and Vaughn in the ambulance and grabs Syd's hand. The two EMTs start talking in a language that Vaughn does not understand. But, that soon leaves his mind as once again Sydney enters his thoughts as she always seems to do. The drive to the hospital seemed to take forever. As soon as they got there, she was rushed off to some room. For hours the two of them just sat there, both of them worried out of their minds.

The hospital

"Agent Vaughn, Dixon. She is awake and is asking for you." Vaughn races over there with Dixon right behind him. Vaughn bursts in the room and Sydney is in his arms in a matter of seconds.

"Are you okay", Vaughn asks worriedly after giving her a kiss. He starts kissing her over and over until Dixon clears his throat.

"I have agent Bristow's test results and we have found the cause. Congratulations agent Bristow, you are pregnant".

A/N: I know that it is long, but I couldn't figure out when to stop. I figured that most people prefer to have a long one than a short one. Anyways good or bad? I need to know how you feel and any suggestions that you may have. As I said that this is only my 2nd fic and my first Alias one so, Reviews are welcome.

L