Chapter Text
The story would have individual arcs that cover a narrower span of time, with time-jumps between that assume life goes on and that things aren't as static as episodic shows try to depict.
Alias came about during an era where Serialized storytelling was finally breaking out from the clutches of Soap Operas. Star Trek Deep Space Nine had finished a run of it, yet Voyager sprinted away from serialized story telling, only occasionally being caught and dragged a few episodes (hirogen) by The Serial Storyteller before breaking free for a season until the next time (pathfinder forcing a subtle 'btw we have contact with alpha quadrant now'). But it wasn't quite there yet, and would be brought to the forefront by Ronald D Moore's Battlestar Galactica reimagining reboot.
Alias combined episodic and serialized storytelling, with both 'mission of the week' episodic, and very, very rarely connected, whilst underneath it, the "B plot" of each episode was serialized.... then the timing (as in, where one episode ends and the next starts) was intentionally shifted off so it kind of felt like, halfway into an epipsode, the episode was over and the next one started. Sometimes meaning that the 'intro credits' with the title of the show are ten, fifteen or even twenty minutes into the forty-minute-runtime. Like the show was resisting being episodic and therefore the guys making it screwed with the running story so you can't watch it in any order (unlike say, Star Trek. All Good Things then Best of Both Worlds is NOT INCOMPATIBLE.)
Anyway. the base idea: will travels into the past, complete with the de-aging.
Time Period One
Sydney and Will are 5-8 years old
Arc 1 (5-6) (1980-1981)
Will Arrives in the past as an orphan with a different last name, and ends up staying with a foster family. He soon realises he's attending the same kindergarten as Sydney, and beffriends her and the bristows. Unfortunately, an incident results in being removed from his foster family, but Jack and Laura (Irina) push to take him in.
Arc 2 (6-7) (1981-1982)
Laura is killed in a car accident... except Will knows that the truth and witnesses Jack's descent into grief and anger, from the weight of believing his 'loving wife' was a spy who didn't actually love him. Despite being looked after by Emily and Arvin Sloane, Will can't help but watch as things almost fall into the patterns he had heard about in his former life.
Arc 3 (7-8) (1982-1983)
While being looked after by a nanny (a CIA Agent that likes the assignment), Will and Sydney are attacked. Will is captured and eventually so is Sydney, and the pair are taken to Europe or Asia. Will Escapes, but gets assistance from Irina to rescue Sydney and Will ends up having to take a life in order to save Sydney, taking a bullet in the process. Sydney is also wounded badly, but knocked unconscious during the rescue. Afterwards, doctors perform an emergency organ transplant from Irina, which Will knows, but Sydney doesn't.
Time Period Two
Sydney and Will are 15-18 Years Old.
Arc 1 (15-16) (1990-1991)
They're in High school. Jack has 'quit the CIA', with a job 'selling airplain parts'. Will seems able to get along with the man, but Sydney is constantly butting heads with her father, and Will realises that he has to remove some of the 'memory-blurring' that Jack had subjected Sydney to not long after returning from the kidnapping several years ago, if she's to eventually be at peace. Also, he's secretly in communication with Irina, and he learns that she knows what Jack did and agrees its time to start undoing some of it, though not all of it, if she's to be safe.
Arc 2 (16-17) (1991-1992)
Jack has fully gone absentee father on them, and the two literally living in the Bristow home without supervision. Will's long-forgotten feelings for Sydney have reared their head even stronger than before in the last few years, and he struggles to keep them down as they have been raised basically as siblings for a decade now. Unknown to him however, Sydney has been fighting feelings for Will for years, having never actually seen him as her brother, but as her best friend and hopes to marry him some day.
Arc 3 (17-18) (1992-1993)
In their final year of high school and planning for college, Will finds he doesn't wish to retread the path of Journalist. He's still not even sure if there's another Will Tippin, given the different last name, though he does look like he remembered, so if he did and there was, it would likely get awkward meeting his other, original, self. However, he receives an offer that he knows is actually from Irina, and is conflicted.
Time Period Three
... yes, if you noted the ages for the respective one and two periods, this is... 25-28. With one arc per approximate period of 00/01, 01/02, 02/03.
Note, however, this gets into the time period served by the show, which was never solid about the 'when' of it actually taking place, except for some episodes mentioning a holiday like christmas or thanksgiving.
The others I had already written the arc descriptions for ages ago, and just entering on here, I hadn't come up with anything, so... not sure.
... ooh. Um. Will's cover job for the following will be basically an evolution of the job he was in when Sydney came back into his life in season 3 (or 5?, there were two episodes, one in each, and he was doing something in construction in it) or so. Also, I'm twisting the timeline, particularly for when the pilot events happen, for this fic.
Arc 1 (25-26) (2000-2001)
With them living together, both with jobs to pay the bills whilst attending college, life for them has settled into a strange semblance of normalcy, yet its very different. Sydney is promoted at work that means she will start to travel around the world for Credit Dauphine, and Will tells her that his own engineering work will be taking him out of state occasionally, and had been putting it off before. But things start to come to a head when, on Campus, Sydney walks right into Will Tippin... a long haired Will, and Will's own instincts he manages to resist facing his original self, isn't to stutter or go 'hey, I've got a twin', but to pull a gun.
Arc 2 (26-27) (2001-2002)
He'd been watchful, ever since Sydney started at SD-6, but there had been no sign of Danny Hecht in their lives. He knew it might be due to the pair, together, attending a different college, even though they (still) weren't a couple. no sign of Francie, whom they had originally met, again, due to the other college. But without the instigating events, he was unsure as to how to go about telling the truth about SD-6 to her. Then, regardless, one day she disappears, and their home is broken into, and he ends up fighting off an assassin, and whilst he's still injured, complete with a fresh bullet wound, she shows up asking him for help, and if he knows someone who looks enough like her she can use the passport. This time, he doesn't want her to go it alone.
She's also not happy at the end of it when learning he did it all with an untreated gunshot wound.
Arc 3 (27-28) (2002-2003)
This is the one where Sydney now does know about Will... to an extent. It's the "season one finale" equivalent, she already learned in the time since the previous year's arc 2 that he worked for someone 'close to us both' to protect her, yet also told 'not jack' when that was her first guess,