An Alternate Timeline bunny

Hey, anyone done any Syd/Will fics?

I've got a bunny for one, but it's combined with another idea.
If you don't want to read, I'm putting the bunny in spoiler tag. if you quote, snip the bunny out for saving on page scrolling, yeah?
Plot Bunny!
1995
Michael Vaughn began his off-book investigation into his father's death after getting his father's journals early. Like, really early - 1995, he's only been in the Agency for a year.
It began with a simple matter of going home early. Or should that be, on time? If he'd stayed later, regardless that he was tired, he never would have caught Brill coming to see him. Brill would have chickened out in handing William Micheaux Vaughn's journals to him so soon. And Michael wouldn't have known that his dad wasn't killed by Irina Derevko in 1979, that it had been faked. He would have met Irina, thinking she had killed his dad. And she wouldn't have been able to disabuse him of that, both trust and that she couldn't chance that Prophet Five could make a move before any of them were ready.

No, the new path, Vaughn quickly learned from the Journals about Prophet Five, and vaguely recalls when he and his dad were running from the group in the mid-70s, when he was 2. They'd been helped by Irina Derevko. Unaware of her past association and cover idenity, he begins to work with her and another. Irina has introduced him to the woman who eventually left the CIA and became the 6th-then-8th most wanted Terrorist known as Renee Rienne.

Concurrently, Will Tippin is a Journalism student, and is affected by a ripple. Had Vaughn not gone home early, Will wouldn't have been driving behind him, and wouldn't have had to stop for a Red light. But he did, and that ripple grew. He observed something he shouldn't have, and unfortunately, he's begun to investigate on his own.

--
1996
Will's investigation has been, informative. It has also taught him much about tracking, and shaking pursuit, and maintaining his own Aliases. An unfortunate side-effect is that, still a student at college he has a constant need for funding, and only a mysterious backer known as "The Man" has assisted him in paying for flights all over the world. But everything he knows, he learned himself. He's not been spoon-fed information, or had information shovelled onto his head. After a year, he knows about SD-6, knows the truth of the group, and only by strokes of luck has he not been noticed by them and killed. He knows that all low-level agents of SD-6 believe that it is a Black Ops division of the CIA. But by chance, while staying in LA with his sister to recuperate from a rough patch of his investigation taking him about South America, he meets this gorgeous under-grad named Sydney through is friend, Francie.

Meanwhile, Michael Vaughn has been under investigation several times for off-book activities, but each time he has been vindicated, his cover stories being 'confirmed'. But he's no longer on the SD-6 case. With his friend, fellow CIA Agent Michelle Moreau both close to a break-through yet close to being found out, however, he's wondering if he can't do more if he leaves the Agency.

At SD-6, Arvin Sloane becomes aware of a possible Security Breach, a mysterious person known only as 'The Investigator' has been noted by other SD cells as having been to various locations of SD-6 operations as little as a week after various missions, and they have no pattern to help identify just how 'The Investigator' is able to do so. All surveillence of the man has proven that the person varies his appearance often, even in the same locations, and they have been unable to use cross-referencing of flight passenger manifests to identify possible suspects, as 'The Investigator' either doesn't use commercial flights, or more likely, uses multiple Aliasses for both entry and exit to each locale.

In South America, Irina Derevko and Alexander Khasinau observe the first mission of their new recruit: Julian Sark. His mission? Find Nadia.

--
1999
Over the last 3 years, Syd has gotten to know Will, and knows that he's got a much worse time of travelling all over the world as a freelance journalist. He's already won various awards, and while he doesn't realise that she knows, she does know how he feels about her. But then, she doesn't feel the same, as she's been with Danny for 2 years. Her job at SD-6 has only gotten busier too, as there have been recent increases of activity with K-directorate and FTL, along with hints of another organisation that they have no information on.

Arvin Sloane, tired of having no leads on whom this 'Investigator' is, whom has also evaded all attempts at capture with increasing distance, finally gives in and assigns the case to Jack Bristow, hopeful that his cover in Airline part exports will help.

Irina and Khasinau are at the start-stages of a plan to gain a lot of rambaldi artefacts, but while they feel they can trust Sark, they are increasingly worried about the behavior of McKenas Cole, who has shown increasing recklessness in recent missions. The plan to raid SD-6 and FTL isn't going ahead yet, because of this. At the same time, Irina receives a call...

Will has made a break-through in one of his other investigations that are funded by 'The Man', and needs help to press his advantage. And so, he calls 'The Man'. The plan they agree to, he will fly out to Taipei and meet Sark at their safe house. Their mission will be to beat SD-6 to the punch, and steal something called 'The Mueller Device'. There's just a problem, one neither realises. SD-6 are on-site when they get in.

Later, while Sark is getting the device to Khasinau, Will is thinking hard about discovering that his best friend works for SD-6, and hopes to high hell she isn't aware of the truth.
Of course, returning to LA, Will greets Syd at the airport and offers to drive her home, wondering if he should say something or not, but then they arrive at her and Danny's place...

--

That's all I got for now.

edit - forgot I put 1996 in the first paragraph, which was headered' by '1995'. oops. :P
2nd edit - put the bunny in spoiler tag, and will post during-season-1 part of the bunny in a second post.
 
Okay, In-season-1 part of the bunny.

Note: I will be using year and episode name, and if between an episode, for example: between '1x02 So It Begins' and '1x03 Parity', I'll just put "Post 'So It Begins'".

1999 - 1x01 'Truth Be Told'.
Will watches from a vantage point in the room, as Sydney moves over to the table with the Mueller Device and photographs it. While Will is in shock from seeing her, Sark doesn't know who she is, and simply waits until she is gone before making a move to steal the device.

After they have left and split up, Will on a fast-jet flight to LAX with yet another Alias of his, Will thinks on Sydney's presence there. It is obvious to him that she is an SD-6 agent. By association, he immediately connects Marcus and her boss, Arvin Sloane, with SD-6, and Credit Dauphine as a front. Hoping to god that she doesn't know about SD-6, he decides to pick her up from the Airport. He doesn't even know if he'll say anything or not, as he's aware of how dangerous it is for him - he's been in not a few shootouts with other SD cell agents whenever they locked onto an Alias of his. But 'The Man' phones him and he's told not to say anything. 'The Man' is aware of Sydney's friendship with him, as well as her association with SD-6. He agrees, grudgingly.

Meanwhile, Michael Vaughn is helping Michelle Moreau evade the CIA in France, and nearly blows his own career but narrowly avoids contact with the CIA team. Michelle takes a new name, along with several new Aliases, one of which is Renee Rienne, and joins 'The Man's organization, for protection.

Jack is made aware about Danny Hecht's awareness of SD-6, albeit the lie told to lower level agents, and that Security section will be dealing with the 'leak'. His attempts to get Danny away are for nought, as he's dead by the time he arrives at Danny and Syd's apartment.

Picking up Syd at the Airport, Will makes no indication that he knows where she really was to Syd, and wonders about the SD-6 agents he did recognise that were also waiting at the gate. Even so, Sydney realises something's going on with Will, and recognises that he seems to be using various methods of evading pursuit. Calling him on it, he puts it off to a recent investigation gone bad and that he's being careful lately. She knows that he'd returned from some of these investigations with injuries, although she never suspected anything and so SD-6 never found out about his injuries thereby avoiding being identified via correlating his injuries with 'The Investigator's brush with SD cells.

He takes her to Danny's apartment, and both discover Danny's dead, and Syd takes off. Will presumes to Credit Dauphine.

--

Two months later, and Will is asked by 'The Man' to assist in creating a cover-story for one of their assets in the CIA, such as including a quote from the agent in a half-fake story that will put their asset far from his mission locale. Will meets Michael Vaughn, who has recently been reassigned back onto the SD-6 case. The two place Michael at a french retreat, and Will joins Michael on a trip to switzerland, where they will be destroying an operation run by SD-4, an operation that Michael knows the CIA would not sanction, despite the benefit. while Will is on the phone to Sydney, Michael first learns her name and that she is grieving from the death of her fiancee.

On and just after the operation, both become aware of the other's investigation into SD-6, and mention of Jack Bristow by Michael accidentally let slip his double-agent status. At this point, Will already knew of Jack's position in SD-6, but not his allegiance to the CIA.

--

It has been three months since she left, and aside from two jobs in that time, Will has turned down most that would have took him out of state, to which Sydney figures that he wants to look after her. She finds that she's been able to be closer to him, and knows that he likes how close he's gotten to her too. While she also puts that down to the same, and the cause being Danny's death, she also feels that on her part it's because she's not lying to him, as she has 'taken leave from the bank'.

Will, however, is very worried, as through 'The Man' and his own sources, he's aware that sooner or later, the Security section of the Alliance will kill her, if she doesn't return to work. His fears are proven true, when one day after having had an enjoyable day in the city, he waits from a distance for her to get in her car and leave the car park, but quickly discovers that Security Section are readying the attack.

As armed as he always has been, he prepares to assist, using a quick and 'dirty' method of balaclava to hide his identity, when she gets help from someone he didn't expect. Jack Bristow. At that point, he leaves, knowing she's in good hands, aware of Jack's double-agent status within SD-6. Having long since Danny's death placed bugs in Sydney's things, justifying it to himself as 'making sure I know when she's in trouble', he gets to hear Jack's confession to her.

The next day, Sydney locates him and sneaks a message to him, and they meet. Sydney needs help - she needs one of Amy's credit cards and her passport.

But Will knows how SD-6 operates.

So he explains, in rough terms, that if she's in as much trouble as it seems, whoever she's in trouble with will know to watch her friends - including Will and his sister, and as Syd can look like Amy if she tried, they will be very vigilant for her using Amy's identity and credit cards. But he's got better. He explains, also in rough terms, that many of his investigations require him to take an alias, and that as she's probably figured out, that he learned from experience the do's and don'ts of evading pursuit or even identification.

Then, he begins explaining that he knows Danny's death wasn't a robbery. He's been in the investigation business too long to think otherwise, given the blackout on cameras in the area. He doesn't add he already knows about SD-6, although she understands that he's missing out a lot, and realises that he might already know, given hints about such and how he acted when he picked her up from the Airport and since.

He'll help her, but he's going with her. With that, he takes her to a safe house of his, and she realises that he's got the equipment to create passports and various identification, as he runs through the process twice for both of them, and helps her change her looks. Affecting a British accent, he books flights from LAX to Japan, then using the others, affecting a Japanese accent, books flights from Tokyo to Taipei.

He realises, in regards to the destination, what it's about, and learns from 'The Man' that a second 'Mueller Device' had been built and put together, although SD-6 never learned about the theft in the first place.

In Japan, Syd and Will meet with Renee, who thanks him for helping Michael get her out. Syd realises that will does more than 'Investigation', even though she already suspects what sort of investigation he does do. Renee gets them some equipment and passes them intel on the place they're heading to in Taipei, including keycards to get through the door - this also makes Sydney put more pieces together, although she's not all the way there to figuring out Will's awareness of SD-6.

Renee finishes with asking Will to give Vaughn her love. Will and Renee don't realise that Syd now has a full name: Michael Vaughn.

The operation in Taipei goes without a hitch, at first, but like in the episode, Syd is caught, only this time on the way out. Will got out, with the device, and after setting it to a safe house, begins the plan to rescue Syd, only this time, he's on his own.

Later, after being woken up by head dunking,. Syd is being interrogated and has teeth pulled. Just as she's about to affect her release, Will breaks in, and shows that while he's learned stuff, he's still an amateur compared to Syd, who not only escapes her chair but also takes down a guard that managed to choke-hold Will. They both escape and get the device, and then set off for a direct flight back to LAX.

On the flight, Will explains to her that he'd first gotten involved in the intelligence world when he was in college working on his journalism course. How later, he gained funding from a mysterious benefactor, and how eventually he began working with them. He'd known about SD-6 for awhile before meeting her, but swears that he didn't know who or where their front company was, nor that she worked for them, until he'd seen her photograph the mueller device 3 months ago. He'd picked her up because he wanted to talk, but wasn't sure whether or not to say antyhign, and what happened with Danny, he didn't want to unload all this on her too. He apologises for bugging her, but it's how he'd been so prepared to help her, and he's aware and thankful that Jack told her about what SD-6 really is. He adds that the various times he'd been injured was evading SD personnel and gotten a bit too close for comfort. But he's sure they don't know it's him.

Later, after delivering the Mueller device to SD-6, Syd goes to the CIA, and while she leaves out the parts with Will, and with Jack, she still details a lot of things that hint towards their parts. While waiting after giving her statement, she is greeted by Michael Vaughn, and she shows surprise, and says that Renee sends her love. He blinks, and doesn't say anything, only smiling a bit. Syd flicks her gaze to the photo on his desk, of him and a women that looks very like Renee. He gets the picture, pardon the pun.

A few days later, after visiting Danny's grave, Syd and Will see Jack approaching, and Will knowingly gives her a smile and walks away after assuring her it'll be a good thing. Jack tells her that her story was authenticated and she's in, and throws in the mention about Devlin to make the point.

--

aaaaaand that it for this bunny's take on 'Truth Be Told'.
 
okay, now I'm on a roll in the outlining. damnit.

1999, 1x02 'So It Begins'
Will and Syd approach the 'blood Drive' van, both intent on sharing intel about SD-6, and all three are surprised when they get in. Michael Vaughn at Will's presence, and vice-versa. Michael lets them know that they can talk freely, there's no bugs. Will explains to syd that he helped Michael get Renee out from the custody of a terrorist cell that she'd angered, but she was kind of wanted by the US Government, although not for anything (yet) big enough to warrant bringing her in, comapred to the benefits they have against both SD-6 and another long-term project he and Michael are working on. Both assure her that she doens't need to know, and they'll share if need be. Compartmentalizing things.

Syd asks if Will is on CIA payroll, and he denies it, then tells them to get on with the intel sharing about SD-6. Syd outlines what she knows, and is annoyed that both Will and Michael are disbelieving that with her help they can take SD-6 out in "Six months, tops."

Michael gets her to draw that map thing, and then shows her the one CIA have compiled. Will shakes his head and adds that it's more extensive than that, as they're only working with SD-6 there, and points out that they are talking about bringing down the whole alliance, SDs 1-12 and their allies, not just SD-6. Having brought his laptop, Will shows some of the partial maps' he's been able to compile, but notes that he's been unable to do it properly, since he's been essentially working alone for each bit of information himself, except for a few occasions.

Michael extends an offer of recruitment pending Devlin's approval, but Will turns it down, suggesting he works better as a freelancer. If he joined, and SD-6 did a background check on him, it would show. Freelance through Michael, wouldn't.

Aside from that and that Will isn't investigating Danny's death, the other change is that Will is brought in for a brush-pass, disguising handing over the disks after copies made by greeting Syd and Marcus, talking about coming back from a little trip himself, and that he saw them in the airport, but as he's got another quick trip out of town and no time to nip home, he asks if Sydney can take his stuff home, he doesn't want to lug his carryon onto a stuff coach with no room for it and end up loosing it.

There is no suspicion from such an encounter, as a day later he has an article published in a local paper, just like he had as covers for his SD-6 investigation trips.

Each bit will be smaller per-episode now, btw.
 
1x03 'Parity', 1x04 'A Broken Heart'
Irina begins making plans, Vaughn is being reassigned from Sydney's Handler, and while Sydney is on operation to Madrid, Will shadows an SD-8 team in Berlin.

Irina and Khasinau, knowing about Sydney's double-agent status, begin planning the raid on SD-6, intent on the timing being such that Sydney, with the tip-off from Will after the fact, will be able to retaliate and kill, or if not, capture, Cole, who is becoming a liability in their own organisation. They are sending Cole after an ampule, but both are aware that they do not really need him to succeed. If anything, Irina thinks that getting it to CIA custody will be advantageous, as Sydney will surely ensure anything requiring it will also end up with the CIA, and if not, they do need it so both aren't with SD-6.

At the LA Office, Vaughn finds out that he's being reassigned to tracking down former Agent Michelle Moreau - whom they are not aware has taken the identity Renee Rienne. After getting thoroughly pissed off at the attitude of his replacement, Vaughn heads up to Canada, to chase down a lead and attempt to push Renee from getting caught. After returning, he finds out about Sydney's ultimatum and his promotion and return to being her handler.

Meanwhile, Will has received Intel from Sark on an SD-8 team in Berlin, that will setting up a German official to then later on blackmail. As the better investigator, Sark wants Will to head to Germany, and essentially catch the SD-8 team in the act, which they can later use as blackmail against The Alliance. He is almost caught by them, but evades notice and succeeds. Returning to LA, he is in the airport and spots Sydney, although she and the SD personnel with her don't spot him.

Arriving in LA, he is informed that the mission she had arrived there for is already over. Will shares his mission details with Michael, whom informs him that his own participation in the whole thing is known only to Sydney and himself - they do not want to draw undue attention as yet, although Michael does share that he could use Will as a source of intel. The previous assistance, handing over disks while in the airport, was a one-off, and that the CIA were already aware of the two knowing one another from the article, and as far as they know, michael had met Sydney awhile ago and asked him to pass something on to her with his things.

1x06 'Doppelganger'
Will heads to Berlin to gain intel for 'The Man', and works secretly with Michael to put paid to Sydney's cover.

In the headquarters of the Hensel Corporation, Will downloads the details about the vaccine inhaler to a thumb drive, and finds the details for the facility in Badenweiler, then heads for Jeroen Schillers' office, where he's sure Sydney already is. putting on a rebreather, he isn't knocked out by the gas, and helps make it seem genuine with Sydney being pursued. In the garage, observing the switch, he greets the replacement, and asks him if he's aware of the Badenweiler facility where they're making the stuff. Sydney is shocked, and so Will adds that she didn't have reason to look at anything like that. He adds that for SD-6's sake, he'll need to be pursuing them out for her partner to see, maybe fire a few blanks. Marcus watches, and Sydney tells him to pick him up and floor it. In the van, DoppelSchiller thinks over this, and wonders just how far the vaccines are.

At SD-6, in the debriefing, they report that the man who chased Sydney and Schiller was a known thorn in their side, who has been shadowing SD operations for the last 3 years, and it is the first time they have observed the one they have been calling 'The Investigator' wear the same disguise. Arvin adds that 'The Investigator' has been getting more proactive, switching from simply investigating the aftermath of their operations to interrupting them. Even though Sydney already knew that Will have been investigating, she hadn't known a lot about just what he'd done, or how good he was that he hadn't ever been identified.

Arvin speaks with DoppelSchiller in private, and asking where the plant was, DoppelSchiller realises what the Badenweiler hint was, and tells him. He is released.

In their secret meeting place, Jack joins Sydney and Michael alongwith the released Paul Kelvin, the one posing as Schiller at SD-6. Jack asks him how he knew abouty Badenweiler, and he explains that this 'Investigator' that chased them out, was only putting on a show, and seemed to know Sydney AND exactly what was going on, and told them about it. He adds that that saved him, as he would have been an obvious plant if he hadn't known what Schiller did. Jack tells them that he's been trying to find out the identity of this Investigator for half a year now. Sydney tells him that 'The Investigator' helped her get to Taipei after Jack told her about SD-6. She hadn't told them where she got the money and fake passport, Jack tells her he assumed she'd had backup papers if she ever needed them. Sydney half-sarcastically comments that she does now.

Back at SD-6, Arvin briefs them on the mission to Badenweiler, and tells them that The Investigator's presence at Hensel Corporation tells him that the man might be on the same track, and to be watchful for him. On location, Sydney greets the CIA team and Will separately, the latter who is there for a single inhaler for his employer. After she leaves and Marcus attempts to trigger the bomb, she's shocked and horrified when he uses a backup detonator and blows the building.

Ooo... Getting tense here.

1x06 'Reckoning'
Will finds the bomb, and finds a 2nd detonator he can't disable. He quickly makes his way to the CIA team and rushes them out, telling them about the bomb. The team barely make it out, all of them are burned in the explosion and injured by debris. Will is forced to call 'The Man' to get them all a lift to a hospital, as the CIA team's own equipment was damaged in the blast. After being extracted, the team reports in, and say that one of their team came across the bomb and attempting to recover it found the secondary trigger, and hence they bare survival, keeping Will's presence secret to pay for his saving their asses. Well, their front's, what with the burns on their backs and how it hurts to sit.

Back in the states, Will meets with Sydney outside of LA, and she notes how bad he is. He tells her that the guy that's funding his trips helped get the team out, and he'd asked them to keep his participation out of their report. His benefactor is also going to make sure he get's medical attention. Sydney tells him what she told SD-6, that 'The Investigator' was there, but was disguised as Danny, and while she'd been able to brush it off while on the mission, the explosion, as prepared for it as she'd been, still gave her flashbacks. (Yes this is a twist on her excuse from the episode) As far as SD-6 are now aware, The Investigator died in the explosion, but Arvin commented that he's not going to hold his breath for confirmation of that.

A few days later, Sydney has her dad's file and after reading it, tells Will during a chat on a secured phone. Will, having already seen Jack's file but also acting on information he'd gleaned from 'The Man', tells her that her dad wasn't a traitor, even though it might seem that way.

Over in Colorado, where Will is having medical attention, he is visited by Sark, who informs him that 'The Man' wishes to meet him, and takes him to a secure location where Will meets Irina Derevko, and learns that she was the so-called traitor responsible for what happened and why Jack had been investigated. Irina, however, doesn't tell him she was Laura Bristow. Will asks her if this meant she now wanted him to work for her, given all the help she'd given him in his investigation. She comments that he had already been working for her. She won't sugar-coat what many of her operations entail, but she doesn't work on the same scale that The Alliance has, and that she had fewer members of her organisation, working more with allies. SD-6, however, lies to their people, and doesn't just blackmail, but creates that which they use for blackmail. Sark explains that all the deaths attributed to himself, Khasinau and 'The Man' are all people who were in their line of work and would be shot as traitors anyway, while SD-6 would kill innocents, like Danny Hecht. They may do monstrous things to other monsters, but not to the innocent. "Off screen", Will is given the 411 on their goals.

Oooh.... Will Will accept or reject? Oooh. Yes, I am aiming for a 'Doing Good Through Evil' thing. but I want their goals to be only explained later on.
At this point, Will doesn't know of the connection between Irina, Jack and Sydney, only that there is one between Irina and Jack. This is the first time he meets 'The Man', although he already met Khasinau before.

1x07 'Color-blind', 1x08 ' Time Will Tell', 1x09 'Mea Culpa', 1x10 'Spirit', 1x11 'The Confession'
Will undergoes some training, having accepted Irina's offer to join her organisation properly. He wont choose to stop helping Sydney bring down SD-6, as ever since Danny's death that goal had become personal for him. He is brought into the loop fully regarding Milo Rambaldi, and what Irina already knows, about the Prophecy, and her interpretation of it. His training goes slower than he'd like, as he's still healing, although with a curious boost from various fringe-medical techniques. throughout he stays in contact with Syd, who informs him that their worm into the SD-6 network has prompted a mole-hunt.

In LA, Sydney finds hidden codes in her mothers' books, and believing it to be evidence of Jack's guilt, shows them to Michael, who upon decoding them, finds that they weren't meant for Jack. Michael contacts Irina, and asks her if she was Laura Bristow.

Sydney speaks to Will while on the plane to Argentina, and he tells her he's got a proper job now, rather than just 'freelance reporting'. She takes that correctly to mean that he's now, properly, working for whoever it was that was funding him before. She doesn't like it, although he assures her that he'd never get into the bad part of it, and reminds her that no innocents are badly affected by this, they don't work like SD-6. He shares that a fuss was kicked up recently, too, but he doesn't know what it is, although it seems to have affected his boss emotionally. He adds that he'll keep an ear to the ground for her. Finished, Sydney tells Marcus that Will's got a new job, and she's really missing him already. They talk about the three months she'd had off after Danny's death.

In LA, Michael has finished decoding the books with the CIA, and unfortunately, Weiss has caught wind of it and taken it to Director Devlin. As aware of the truth as he is, Michael is still shocked at how his father's name was one of the names. He is still unsure of how to proceed, given that he has worked with Irina in the recent past.

After Syd returns from a mission to greece, Michael meets with her and shares that he left out one of the names from the list of agents killed mysteriously, and tells her that while he's with her on not reporting Jack, as he's got his own evidence contrary to hers, first, he can't use it as his source is questionable, and Weiss already went ahead. They have a meeting on Monday.

that night, Will speak with Sydney, and tells her that whatever the outcome, he's needed to deal with SD-6, both to help provide her with cover when she's on CIA missions, and when they need to cover each others backs on missions for SD-6 that they sabotage. Afterwards, he speaks with Michael, who tells the intrepid investigator that his father was one of the agents who hadn't been killed by the agent, and infact worked with said agent in faking his death, and that Michael himself worked with him. Will asks if that person was Irina, and Michael, not yet realising that Will has been told about the books specifically, confirms it. Will knows that Jack got those books for Laura Bristow - Sydney had told him ages ago. Will confronts Irina, asking her if Sydney is her daughter, which she confirms, and tells him that Truth takes time, and this truth, Sydney needs to learn on her own.

1x12/13 'The Box'
McKenas Cole meets with Khasinau, who informs him that he has an extra guest on his team, and introduces Will, using an Alias, as 'The Investigator', to Cole. In private, Khasinau tells Will that Cole has become a liability, and that if necessary, Cole must be taken out after the mission is completed. His goal however, aside from that, is the plant a worm into the SD-6 network, that unlike the CIA's worm, wouldn't hog bandwidth and therefore get noticed.

In LA, with both Jack and Sydney out of the office, the group are given the go, and break into SD-6. The introduction of Will as 'The Investigator' to the unstable Cole however, bites them in the butt, as during Arvin's interrogation, Cole shares that he's got this new guy on the team, one put there by 'The Man', which he doesn't much like. Someone, he hears, ahs been a thorn in SD-6's side for a long time, or so he heard. He tells Arvin that it's The Investigator, whom Arvin dismisses as having died in Badenweiler. Cole tuts, and shares that The Investigator probably knew about the bomb and disarmed the main detonator, and got out in time to survive the blast.

Arvin, seeing an opportunity, suggests a trade: If Cole agrees to hand them The Investigator, he will hand over the Rambaldi Ampule himself. Cole, pissed off at The Investigator for some reason, takes time before he agrees, although he's also pissed off that someone's messing with his people.

Will, along with the british intelligence mole, find Sydney and Vaughn, only Will knows that Toni is SIS, and tells her to be careful around Cole, if he found out, Cole could, although he's certainly unstable enough that he hasn't needed a reason to shoot anyone before. Sydney and Vaughn realise that it's Will, although they don't name him. They decide that they need to bring Syd in, and let Vaughn do his thing unhindered. So Toni and Will bring Sydney in, and Vaughn disables all the C4 explosives.

When they receive the order to kill the SD-6 employee's, Will turns on his people and knocks their aim off, even as Marcus shoots the others. Will leaves before they can stop him, and Sydney runs after him. Together, they get Cole and the ampule into CIA custody, and Will leaves while the CIA team are distracted, while Syd returns with a story that the pair had overpowered her and ran and that she doesn't know why 'The Investigator' stopped his teammates from killing them.

Afterward, Will meets up with Sydney, who's sort of pissed off with things, and the kind of late warning from him. He shares that now SD-6 will be intensely focused on this and it's 'The Man's plan to use it to destabilize The Alliance, to fracture it through corruption until they can all be dealt with by the CIA and various agencies. Sydney accuses him of becoming a terrorist and simply working to remove a competitor, prompting him to leave without letting her retract it, even as she hates having said it the moment she did.

1x14 'The Coup', 1x15 'Page 47'
Will, caught between working for Sydney's mother, and not being able to tell her that her mom's alive, and not only that but still having not talked to her since her accusation, which hurt him more because he wasn't sure about it himself, hears from Michael that Sark attacked FTL at the same time. Aware as he'd become about the players, Will's conflict over his participation only increases, as he can't honestly say to himself that FTL did or didn't deserve it.

Later, he's tasked to negotiate with K-Directorate, and knowing that Sydney will likely be watching, along with Marcus, he tries his best. While Ilych Ivankov is dismissive of him due to his age, he reminds Ivankov that he is experienced, and had, prior to working for his employer, successfully evaded SD-6 without any back up of any kind, and no one, SD-6, or K-Directorate, have any idea who he is, Age is of no particular matter. Also, it is in the best interest of K-Directorate for them to agree to The Man's offer for the Rambaldi journal they acquired in Argentina, for $100,000,000 in US Currency. Ivankov turns down the offer, and is about to leave, but Will realises why Irina sent him, and forces the issue by having one of his guards shoot the man. The assistant, who is the immediate successor to the post, agrees.

After hearing the cafuffle outside, Will leaves, sick to his stomach at having just ordered a man's death. Later, he calls Sydney, and he confesses that he thinks that's why he'd been assigned, not Sark, to prove he could be more than he had been so far in the organisation. If, even if he wasn't pulling the trigger, he could still order the death of men who were not saints by any definition. Surprised by his call, Sydney tells him she was sorry for what she'd said, and realises just how much it affected him, and the two talk.

A few days later, after Sydney is briefed on a mission to recover the Rambaldi Document, she's talking with Will, who tells her that his boss already used her contacts in K-Directorate to make copies of all except a blank page. He tells her to expect a courier delivery of an otherwise perfect forgery of the blank page, and asks her to replace it, and to keep hold of the original. His boss is only going through with this as 'The Man' expects SD-6's interference. Will assures her that he'll give her plenty of time to knock out any of the crew and photograph the rest of the pages for the CIA. Sydney asks him if he knows why 'The Man' has been doing things the way he has been, and Will tells her that, there is a plan, and he knows a bit of it, enough to get him on board in the first place, but he can't share it. But it involves the CIA, and it's not a bad one, not when it helps get rid of other, greater, threats.

After her return, Will learns from Michael that they want that page, and plan on having Sydney go to Sloane's house to get it. Feeling mischevious, Will returns home, and when Sydney tells him she's been invited, along with a guest, she asks him along, partly because she needs a friendly face, and that she wouldn't want Francie to get all ratty with Sloane being a slave driver, which both of them know she would.

Attending the dinner, Will shares stories of travelling the world and of his articles from all over, and is pleased to hear that Emily had become a fan of his, especially that she was deeply affected by the various ones he did in Africa. When Arvin notices he has the slight scarring of bullet wound to the arm, and a burn on the back of his neck, Will comes up with a story about being shot by some warlord in Africa, who didn't like how his articles had portrayed his home, and how the burn was from being close to an exploding building a few months ago, while doing a story in the middle-east. All stories that he'd managed to use at the time as cover.

That night, Sydney goes to the bathroom, instead of Sloane's office, and waits for a little bit, then returns to the table. Jack finds how quick she seemed to be rather curious. Afterward, he confronts her, believing she hadn't made the switch, but she hands him the real page, which he notices by feel is different from the fake that the CIA handed over.

Meanwhile, Will receives a message from Irina, she suspects that the truth about the car crash will come out, she feels it in her heart. She pulls him from LA, so that he doesnt have the trouble of knowing all while she still discovers it in drips and drabs.
 
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