This is the single most fucked up fix it fic you will ever read because technique isn't a fix it fic. Bear with me as I attempt to turn midnight shenanigans into readable and understandable literature.
Warning: Character Death, Character Resurrection, Homosexuality alluded to (If you don't like, don't read), Heterosexuality alluded to (same warning applicable), Cross-over, the writer (viable warning. All who enter here take heed), One-shot (because you sometimes need to be reminded), gross disuse of parentheses (can't you tell that I love 'em?), Shifting Doctors
Pairings: Doctor/Master (in that order), Phil/Darcy, Master (Harry)/Lucy
I don't own Avengers or Doctor Who. Surprised?
The first time "Phil Coulson" dies he is three months old and the time period in which he was born disappears. The Year That Never Was never happened and he was never born. Except for the fact that Phillip John Saxon was stolen by a Doctor (THE Doctor in fact), from his cradle the same day the Doctor collapsed the time stream. This, of course, causes the world to forget. Phillip was stashed, in stasis, deep within the TARDIS for approximately 30 years (Doctor's linear timeline). He was then given to the Coulson couple who lived in the 20th century A.D. And this is where he grows up, unaware of his dual hearts and lineage until he the age of ten. When he is ten everything goes to hell in a hand basket and does not return to normality for a good long while.
Phil learns how to get anywhere without being noticed and officially becomes Phil J Coulson, a human, and quite the average human. No one notices him and he likes it that way. He skirts around the edges of everything, unseen but powerful. He quickly learns how to know everything, even the things no one wants him to know. The computer becoming a household object in the 1970's makes his job infinitely easier. Then he discovers S.H.I.E.L.D and cannot help but be fascinated. Maybe they would know the answer to his two-hearted problem. Slowly he played his parts much looser, allowing S.H.I.E.L.D to catch on and offer what he wants: a job with them. It takes 19 years of careful planning, in which Coulson perfects his stony-hearted demeanor, for someone from S.H.I.E.L.D to be sent. Coulson denies the job offer immediately. They did it wrong, he wants Agent Fury (who is well on his way to becoming The Man in Charge) to personally invite him to join. He has watched the man's path with much interest, and if he survives to be Senior Agent nothing will stop him from getting to the top.
Eventually he hacks S.H.I.E.L.D's database and makes it Agent Fury's job to convince him to join. It is cheating but Coulson does not plan on waiting forever for things to happen. If he wants to make it happen, he will. He makes Agent Fury work for it and on the day Fury becomes second in command of S.H.I.E.L.D Coulson accepted the offer. Less than 3 years later Fury and Coulson where second to none, but he still kept his uniqueness a secret. He brings in good agents by the dozens and excellent agents by twos. Then Avenger's initiative becomes his baby even before Fury considers the idea, and nothing will stop him from helping save the Earth, not even stubborn heroes. Around this time he also starts remembering blue boxes and strange men who wear pinstripes, and aged centuries in seconds. The job is his obsession and it is not long before he brings in the first fruits of his labor. Clint and Natasha, human and dangerous, trained assassins and dripping ledgers but Coulson thinks they could not be any more perfect. Next comes Tony Stark, insane but a living genius, who fights because living on Earth is boring. Coulson smiles and forces whispers of "Just like the Doctor" out of his mind, already securing a way to make him sign on to his plan.
Captain America is a quick choice, his one split second decision. It really helped that Coulson actually has those cards because Captain America's golden years were when he was growing up, playing fan boy and making everything seem like common sense to S.H.I.E.L.D is a challenge he relishes. With him comes Bruce Banner who occasionally turns into a green giant when enraged. Thor is another accident but with a pinch more pre-planning. Darcy is amusing and Coulson almost forgets about the "little" dual hearts issue when she calls him the I-pod stealing ninja agent.
The second time Phil Coulson dies he is approaching 83 human years but he appeared to be only in his late twenties or early thirties (his birth certificate says August 28, 1989). Coulson stares down at Loki, completely and utterly calm. Death would be lovely, to finally pass beyond his handmade web of lies, a prayer finally answered. That dream ends quickly when he feels something bubble up inside him. It threatens to break through him and all he can do is staring hazily forward as Fury tries to talk to him. He fights it tooth and nail because he wants to die and whatever this is, it wants him to live. He is still fighting it when the paramedics arrive and declare him dead. He wants to shout at them, tell them they are right and he is finally gone, but he can hear the twin beat of his hearts still going.
As they pick him up to remove his body a familiar claxon sounds and two men appear with a blue box that had not been there before. One is wild haired and wearing a bow-tie, suspenders, and a tweed jacket while the other wears a perfectly tailored black suit that reminds him faintly of blood and screams, but mostly of safety.
He distantly hears them speaking and feels it when he is dropped, although he does not see the angry glares exchanged between the men or the confused look on the emergency personnel's face as they wander away. "Are you okay, Phillip?" The bow-tied man asks. He does not answer, still fighting life.
"Stop fighting!" The other commands harshly, and Phil does. A bright light envelopes his vision for a split second before a peaceful darkness descends.
Phil never hears the Doctor tell the Master, "He takes after you. The regeneration issue only happens to your family."
"I seem to remember a few issues with your Fourth." The Master snaps as he picks up his son's prone body. "Besides I'm not sure he is mine." The Doctor rolls his eyes, almost not believing the man.
"Do the suits, hair, or overall general demeanor not tip you off?" He huffed, opening the TARDIS's door for the Master and his bundle. "I could do a tissue scan..." He offers cautiously. It has been far too long since he has spent time with the Master and he can no longer tell when the other is joking with him. The Doctor follows behind the Master immediately, going straight to the TARDIS's core and initiating takeoff.
The Master sighs and settles the man on the couch generously provided by the TARDIS, "Not necessary. Lucy left her mark." A hand fondly brushes the hair across Phillip's face and settles on his temple. "A little push is all that is needed?" The Doctor looks up from fiddling on the TARDIS.
"Oh, um..." The Doctor blinks trying to figure out what he was just asked, "Yeah. Smallest push you can manage, his bio-data and mind are a bit unstable but they should level out after the push." The Doctor watches as an expression similar to love appears on the Master's face. It is not love because this shadow created from fond memories of the Gallifreyian is incapable of even loving his own son. Fingers alight from the dying man's face and the Master smirks as he backs away. Artron energy lights up the console room with a muted blue tinge for a split second and two aliens silently watch as one of their own gains a new face. Phil's hair thickens and flesh appears where he was previously bone thin. The suit, previous well-fitting and immaculate strains under the shift in mass. The chin softens and becomes less prominent as the two stare fixated. Gradually the changes come to halt and the Master grins.
"Looks like I'm done here." The Doctor's gaze is ripped from Phillip's second regeneration to the Master. "Surely, you didn't expect me to stay, dear Doctor?" The Master laughs and a wave of nostalgia overtakes the Doctor but it dissipates with the Master's spectre. The Doctor had hoped that his friend would stay but had known at the same time that he would not. It was disappointing but not crushing. After fiddling with the controls for a long while the Doctor wandered over to where Phillip was sleeping. He was slightly concerned because Phillip did not seem to be waking up. First regenerations were always rather traumatic but with who this Time Lord owed his lineage to The Doctor had expected a quick wake up time. Only once he was really close did he notice that what he had assumed was sleep breathing patterns actually seemed to be awake breathing patterns.
The Doctor grinned, "Glad to see you're awake. Most of us don't take so well to our first regeneration. Now, now don't worry-the TARDIS will take good care of you. Unfortunately your father couldn't be around for this but you know being dead does end up putting a crick in the best laid plans." He would have rambled on if Phillip had not opened his eyes. They reminded the Doctor of the Master's eyes in his third regeneration.
"I've heard worse." The newly regenerated Time Lord stated plainly. He was unimpressed with his captor's blunt honest. The man in the pinstripe suit seemed content to blabber on and on about anything and everything, and was readily distracted.
The Doctor wondered with a noncommittal, "Hmm?" Curious enough to desire an answer but not curious enough to ask.
"Stories behind kidnapping me." Phillip stated plainly. The Doctor gave him an incredulous look from his place halfway across the consul room.
"But I haven't kidnapped you. Honestly, why is that everyone's first response! 'Oh, you kidnapped her!' 'Oi, you kidnapped me.' I've never kidnapped anyone." The Doctor sulked, "The door is even right there, you could walk out if you wanted to-though I can't say I recommend it. Something tells me that walking into the vacuum of space after being newly regenerated is a not very bright idea." Phillip did not move from the couch.
This kidnapping definitely took first place for 'eye roll worthy', "Then return me to the Heli-carrier. I have work to do." Phil was quite assured that the man, whoever he was, would not return him to S.H.I.E.L.D.
The Doctor's face fell and he looked down at his scuffed trainers, "Go look in a mirror and then tell me if you want to return." The voice was soft but it carried and the words seemed to trigger some kind of mechanism within the holding area. A smooth, expensive looking mirror slid out of the wall and presented itself to Coulson and he took a look. The man he saw in the mirror was not someone he recognized.
Without looking away from the mirror he asked, "What did you do?" Phil was calm, this might not be covered in S.H.I.E.L.D training but he had two hearts, he could deal with this in a level-headed way.
"Nothing. Your father gave your DNA a little push because you were dead but you weren't regenerating like we're supposed to and, "Voila! Sorry about the suit though." Phil held up his hand for the rambling man to stop.
"Start from the beginning and include your name." He commanded the man, turning around. He took in where he was being held and suddenly knew that he was in way over his head.
The Doctor did not seem surprised by his demand though, "I'm the Doctor." He starts simply and Phil nods. "You're Phillip John Saxon, the son of Harold Saxon and Lucy Saxon, you kind of don't exist." The Doctor looks embarrassed. "I am...uh...kind of lonely and your father took over Earth with the help of a Paradox Machine," He cuts himself off suddenly, "You know what? We might want to sit down for this; it's a really long story after all." Phillip acquiesces because what he has heard so far has the ring of truth to it and it is a bit much to take in.
"Anyway," The Doctor begins again after they have sat down, "You're Harry and Lucy's son. Harry is actually like me, a Time Lord and when he procreated his son was also a Time Lord. You have two hearts, extended lifespan, and the ability to regenerate plus more. He tried to take over Earth using a Paradox Machine and succeeded. You were born while the Paradox was active making it so that when the Paradox ended you should have ceased to exist. I'm not immune to flights of fancy though and so when the Paradox was collapsing I kind of stole you from the crib and kept you safe until I gave you to the Coulsons...
The rest, as they say, is history.