Warning: This video is actually pretty horrifying and gnarly. Turns out that Agent Coulson's return from the dead after The Avengers wasn't quite as straightforward as he (and we) were originally told, judging from this clip from last night's Agents of SHIELD.
The video above actually shows the seventh surgery Coulson had after he was stabbed by Loki in The Avengers. Turns out, according to Dr. Streiten (Ron Glass!), after Coulson got ganked, Nick Fury "moved heaven and earth" to bring him back, authorizing procedures that no reputable doctor would allow. Lots and lots of weird superscience, basically — but it's still unclear what Coulson is at this point. He's obviously mostly organic, but he's also kind of a super-zombie.
In any case, the procedure we're witnessing above is the tail end of the resurrection process — he's already alive in it — and is more concerned with reprogramming his brain, to make him a happier guy. Coulson had to be conscious during all of his post-mortem surgeries, so they could monitor his vitals, and now he's lost the will to live, as evidenced by him saying "I want to die" over and over.
So they're not only giving him the fake Tahiti memory that he keeps remembering, and the pre-programmed "It's a magical place" response when anybody brings it up — but also, changing his brain around so he will want to keep going.
What we still don't know is, why is Coulson so important? Did Nick Fury go to so much trouble to resurrect one agent purely out of sentimentality? Also, in this episode, after Coulson is taken prisoner by Raina, the "flower dress" lady, Nick Fury puts all SHIELD's resources on getting Coulson back, to an extent that startles Agent Victoria Hand. Is that just because Nick Fury doesn't want anybody to know how he brought Coulson back? Or is there something else about Coulson that Fury wants to keep secret?
This episode draws a bit of a contrast between SHIELD and Raina's as-yet-unnamed organization, which created the Centipede super-soldiers. Raina and Po (who snuffs it in this episode) both work for the Clairvoyant, who is some kind of telepathic precog dude who sees everything except for the secret of Coulson's return from the dead. And the Clairvoyant has seen an end to SHIELD, apparently. In any case, both SHIELD and the Clairvoyant's people do weird science and experiment on people and use their soldiers in a callous fashion — so what makes SHIELD better than the Clairvoyant gang?
A few differences suggest themselves: SHIELD is slightly less callous about discarding its people — in this episode alone, Po gets killed for basically no good reason. And various Centipede soldiers have been killed via "kill-switch" in the past. Also, Centipede uses those eyeball cams to monitor and control people, killing them remotely — including Mike Peterson, who's not actually dead, as it appeared after the previous episode, but rather the latest Centipede stooge.
In any case, Raina wants to learn the secret of bringing her "soldiers" back from the dead — although given that it took seven surgeries and a shitload of resources in Coulson's case, wouldn't it just be easier to recruit new people? At this point, Centipede doesn't seem like the smartest organization in general. They rely on people like that alien merch dealer Vanchat, who's easily broken by Agent Ward, and their whole plan involves creating supersoldiers who are somewhat stronger and tougher than an ordinary person — but not tougher than 100 ordinary people.
But because SHIELD doesn't coerce people the way Centipede does, they actually had to do brain surgery on Coulson so he would want to keep doing their dirty work. That's better, right?
The meat of this episode has to do with Coulson questioning what he's been told by his superiors, but also whether this was all really worth it. He didn't just die in the line of duty, he lost the chance at happiness with that cellist he was in love with. The crux of the episode is when he starts collaborating with the enemy, the people who he thinks killed Mike Peterson, because he's that desperate to get answers. He allows them to use their mind probe on him and stops fighting it.
What saves Coulson from revealing secrets to the enemy and becoming a massive traitor is his faith in Skye, who has yet another one of her "everybody doubts Skye and then she comes through" storylines in this episode. It's sort of interesting that Skye triumphs over a challenging situation (the haxx0r can't use any computers due to a bracelet) by pretending to be Melinda May, who Skye thinks is sort of a mean fascist. (Melinda May throws Skye off the plane, but anybody who's seen television will know it's so that Skye can go do her own thing, without SHIELD looking over her shoulder. But she's mean about it.)
Coulson's recruiting of Skye can be seen as an act of rebellion against SHIELD, the hidebound rules-oriented organization that he subconsciously knows screwed with his head. SHIELD wanted a happy Coulson? They got a Coulson who was so happy, the rules didn't entirely matter to him any more. He's so damn happy, he's willing to entrust everything to an anarchist with nice hair. That's what you get when you poke someone's brain for too long.