Fury kept Coulson quiet and classified the same way you drop dye in the water to see where it goes colours. Level 7 to know he exists, Level 10 eyes only to know how.
That 'welcome to level 7' line in the first episode is a weird choice if all you need to say is he got injured and survived. Why not tell the whole organisation that?
Well we saw who really really wanted information on miracle survival, and he turned out to be Level 8. The level 7 info was bait that got him chasing the level 10.
Problem: Coulson didn't know he was bait. Which made him more plausible, but left him thrashing around churning up the pattern by asking questions everywhere. By the time it became crucial to know who knew what, he'd stirred it up but good.
But who did Fury think he was hunting in the first place?
Well the Avengers think Coulson is dead. That's specific and seperate from that general Level 7 bit. And the Avengers would really really want to know about Coulson.
Fury? Really really wants to know if Tony Stark is still in his system.
And what are the odds that Stark of all people could find out about Coulson, classified as heck as he is, and then just shrug and decide secrets are in this case cool?
(If Pepper cried... We can be pretty sure Pepper cried. Is Tony ever going to be cool about things that make Pepper cry?)
So there's dye in the water and Fury is expecting Stark to come up with it all over his hands, if and only if their efforts to get JARVIS the hell out of the files failed.
But what he gets instead is Centipede and the Clairvoyant. And they're not subtle. As it turns out, the Clairvoyant can't afford to be, he's on a clock.
Centipede have access to pretty much every source of superpower known to man. So does Stark. They're researching, specifically, how to stabilise Extremis. So is Stark. And it's Pepper, so he's real motivated. Motivated enough to do what Centipede did? Well they're weapons manufacturers working in human enhanciles to make a private army, say, to privatise world peace.
So. Is. Stark.
And Fury doesn't know if he's the guy to do human experimentation, because Fury didn't know he was the guy to come out of the desert all superheroic, and SHIELD's profile on Stark is excessively unflattering.
Hypothesis: Right up until the Clairvoyant tipped his hand, which was after Fury 'died' and SHIELD went splat, Fury had good reason to suspect Tony Stark was behind Centipede.
He had the money, he had the tech, he had the motive, and he'd been all over SHIELD files so he sure as hell had the data.
We the viewers can assume he wouldn't go there, but lets face it, in universe the difference between him, Quinn and Hammer is... style.
Also competence. But that just meant his fuckups were much more spectacular.
So if data is leaking when it shouldn't, and Stark isn't kicking up a fuss about it, but someone is interested in the same areas of research? You can assume it's nothing to do with Stark, or you can assume Stark got serious. Or, of course, that Stark is the one being betrayed, again, by someone in the inner circle, again. Possibly someone who just had an enhancile poured into her, that seems to be making others really publicly unbalanced.
Fury didn't tell the Avengers. That's the only fact here. But if he specifically did it to see where the data went, he got a lot of very criminal splash really fast.
And ultimately they led to HYDRA.
Which is more plausible, to Fury: that he'd missed HYDRA in his own house his entire life, or that he'd missed it in Stark's?
So by the time Winter Soldier happens, Fury is paranoid as hell, not talking even to his Level 8s, for what turns out to be good reason, not picking up the phone to Coulson, which... is either really stupid or very strongly suggests he was chasing leads personally that he didn't trust to anybody else, and really looking forward to having the Insight carriers at his disposal when he did finally track this trail, suggesting he expected big game at the end of it.
A trail being screwed up by Coulson's personal issues, as well as the Clairvoyant's.
But a trail that could easily, by money and tech and issues involved, have led to Stark.
I've read a lot of fic that shows the Avengers blithely digging through classified data and kidnapping Coulson to safety and getting free of Fury and SHIELD and Fury being happy about this because now they're out from under the WSC, who recently nuked New York.
the thing where his own people were willing to nuke New York really pulled the rug out from under Fury, and Stark hacking SHIELD is a significant problem from the point of view of anyone, you know, not Stark. We know Iron Man's the good guy because of decades of comics, but Fury don't necessarily know it even from his actions since Afghanistan. Stark gives so many good reasons to be *facepalm* and some to be legit afraid.
He didn't turn out to be HYDRA, but, how to know that, before they targeted him?
And even after that, that just means there's two powerful non government organisations with very divergent views on how to ensure world peace through ultratech.
So a move that big on behalf of the Avengers, before SHIELD went splat, seems to me likely to get a very different, more hostile, answer for entirely legit reasons.
And now SHIELD has gone splat, everyone, every single side, governments, SHIELD remnants, and HYDRA, can look at Stark setting up a private army and really really worry.
Because yeah, we like him, but really?
The persistent portrayal in fic of Fury as Shouty Boss Who Doesn't Understand is just kind of... I don't know from comics, I don't know if it's coming from somewhere, but the guy we see in the movies is the guy who will turn up in person to set out the welcome wagon, who will tell Stark things about his father and his past that he must not have had the security clearance to know before, who will send his best people to help when Stark is sending up every behavioural warning flag by giving away his stuff and acting like that at parties, who will believe in heroes and buy them the time they need by being the one to pull the trigger on his own WSC driven people, and who will turn up in person for rescue missions after SHIELD falls apart. He's a guy who cares about Stark, personally. And Stark never gives him trust in return. Has his reasons, but still. Fury keeps reaching out, Stark keeps being Stark about it. All Fury does about that is be supportive again.
I haven't really read that guy.
But if we start from the idea that Fury keeps secrets because he believes it keeps the world safe, he's got stacks of reasons to not trust Stark.
I think fic could do better by him when addressing the whole Coulson secret. Just act like he's got a reason and see Coulson as the company guy who is really dismissive of the bits of SHIELD that went private after the fall. That fic plays out much different.
And probably with less Clint kisses, so my reading preferences could be heavily slanting what I seen there, but still, that's the challenge of ongoing canon, how can we keep the 'ship without throwing out the new episodes. Do the two guys as we know them now still fit together, or did we just AU them forever. Not knocking the AU, just wonder how the new canon could work.
Also think the future new canon is going to work much less well without noticing where there are actual tensions in the existing story.
But, today's conclusion: It makes sense for Fury to worry about Stark post Avengers movie, because he set out bait for Stark and got nibbles from Centipede, the Clairvoyant, and HYDRA. Sorting out where they weren't connected could easily take more time than they had.
Meantime, Coulson was very lively bait, which went poorly for a great many people.
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