Agents Of S.H.I.E.L.D. is a spin-off television series adapted from the ever so popular franchise know as the Marvel Cinematic Universe. Agent Phil Coulson was a fan-favourite supporting character and it seemed like a no-brainer to give him a spin-off. One problem, Loki killed him in the Avengers. So Coulson gets resurrected through mysterious means that unravel as the show progresses and then we have a television series. SPOILERS FOR AGE OF ULTRON
What The Show Wants You To Believe
Some time in the past, S.H.I.E.L.D. discovered a Kree body and extracted its bodily fluids to create a magical resurrection serum. After Coulson died, Fury used the serum to bring him back to life. Coulson feared the side effects that were demonstrated from previous patients and chose to have his mind wiped through the T.A.H.I.T.I. Project to cure him.
Coulson eventually remembered and began demonstrating the symptoms he feared. After months of hard work, he figured out the carvings he was making were a map to a Kree civilisation. This knowledge seemed to cure Coulson and everyone else. The civilisation housed the Inhumans and started the big arc of Season 2.
What Actually Happened
Coulson has been dead the whole time and has been imagining the entire series in a state of limbo. There's a lot of evidence to back this up, don't worry. We've got a lot to cover in this article so I'll get right to it.
Think about it, a magic serum that we've never heard about before has the ability to resurrect people but also with dangerous side effects that can only be cured by memory wiping. This could just be convenient writing on Whedon's part, or this could be Coulson's sub-concious coming up with a way to go back into society and do what he does best, save the world.
The Films Do Not Acknowledge It
The thing that has always bugged me is the fact that the MCU films completely ignore the events of the show. Coulson has been resurrected for awhile now, I think it's about time they knew. In fact, I'm pretty sure they're the only ones who don't know. Or, does no one know because he actually hasn't been resurrected.
The films simply do not acknowledge the show. When Nick Fury gets his helicarrier in Age Of Ultron, he doesn't say "Thanks Coulson for this helicarrier", he just acts like he had this in his garage.
Facts That Just Don't Add Up
Something that Season 2 has done is try it's best to connect with Age Of Ultron. There was this useless sub-plot called the Theta Protocol that's sole purpose was to connect to the Avengers sequel. There were just some things that happened that contradict certain events in the film.
Gonzales states that he trusts Coulson because he prevented Ultron from killing thousands. Ultron didn't want to kill thousands, he wanted to kill billions. Gonzales, you're a little bit off with those figures, way off to the point where there isn't an excuse.
Maybe that's a nitpick, but I have another bit for this point. In the show, Coulson was the one who tipped off Maria Hill for the location of Loki's sceptre. Now the film is a different story. The Avengers had been tracking down HYDRA bases for quite some time and when they reached Strucker's lab, they seemed surprise that the they found the sceptre.
This indicates that Coulson's mind is still loosely connected with the real world while remaining disconnected to the point that he gets facts wrong.
Joss Whedon Even Said So
A lot of people come back in The Winter Soldier. It’s a grand Marvel tradition. Bucky was supposed to die. And the Coulson thing was, I think, a little anomalous just because that really came from the television division, which is sort of considered to be its own subsection of the Marvel universe. As far as the fiction of the movies, Coulson is dead.
Joss Whedon has told us that Coulson is dead, isn't that evidence enough? Until the films and the show are properly connected, Coulson's resurrection isn't technically canon.