Coulson lost his parents at a young age, as revealed by Raina in episode 11. It certainly sheds some light on why he's so adamant about not letting Mike Petersen die in the pilot, specifically referring to making sure Ace doesn't grow up without a father.
Simmons' comment on being "ready for a Journey Into Mystery" is used as a Mythology Gag to Thor's debut in the comics because it's also a Call Back to the fact that Thor's appearance in the MCU is what really took things from "billionaires in metal suits" to the "whole new world" of alien technology. And the first film in the Marvel Cinematic Universe to be released after the pilot first aired? Thor: The Dark World, which will be delving deeper into the Asgardian mythology of the MCU.
When we first meet Skye, she's a computer hacker trying to take down the most powerful Government Agency of Fiction on Earth. Naturally, she lives in a van: mobile with no address.
Ward points out that someone really wanted their initials to spell out SHIELD. Makes perfect sense since SHIELD was founded by Howard Stark and Agent Peggy Carter, both of whom had tremendous respect for Captain America.
In "F.Z.Z.T.", Blake orders Coulson to dump any "infected cargo" if necessary. Coulson is, therefore, not truly disobeying orders when he does not throw Simmons out of the plane because people don't count as "cargo."
May practicing tai chi in "The Hub" makes more sense after watching "The Well". Apart from the obvious martial arts applications, she uses tai chi as a form of meditation to relieve stress and maintain her stoic demeanour, and deal with what happened to her in the past.
They mention that only Barton (Hawkeye) and Romanov (Black Widow) never needed extraction plans in "The Hub", which is true if you watch Black Widow's first scene in The Avengers.
Why Nick Fury and such go to such efforts to help and protect Coulson makes sense after rewatching Dollhouse's penultimate episode. He's Nick Fury's closest friend. He's family. Wouldn't you do anything to save your family?
In "Seeds", when the team is trying to revive Seth, the fact that Coulson is the one to tell them to stop defibrillating him is especially significant given how traumatic his own Back from the Dead experience was.
Stan Lee's character is the only one to fall for Simmons' over-complicated cover story in "T.R.A.C.K.S.", which makes a lot more sense once you consider that - by dropping in a lot of expositional detail at odd moments - she's talking a lot like a character in a Golden Age comic book.
Some people complain that Coulson's outrage about the truth of his revival is hypocritical for someone who used to be totally cool with all S.H.I.E.L.D.'s secrecy. But if you watch closely, you'll note in previous episodes like "The Hub" that, while Coulson is fine with people simply not knowing about stuff that doesn't involve them, he's not cool with deceiving people or hiding truths about things that directly involve their well-being. So while he told Skye to just deal with not being cleared to know about the mission, he was outraged at them keeping the plan from Fitz and Ward whose lives were in jeopardy because of it. This is also why he's fine with keeping the truth of the Guest House from everyone but Skye. It affects her directly, but not the others.
Even when the agents enter Thomas Nash's chamber, there is a subtle hint that he's just a prop and not the real Clairvoyant: the voice does sound Creepy Monotone, but still has an intonation, for example it sneers at Coulson. It is not Machine Monotone, as a computer voice would have been.
After The Reveal of Captain America: The Winter Soldier, Nick Fury's reason for creating Team Coulson becomes perfectly clear: Look at the people he assigned to the team (not counting Skye and May, who were recruited by Coulson): Agent Ward, while apparently a loyal SHIELD agent, doesn't work well with others and views himself as the whole solution to any problem. In short, he's something of a Cowboy Cop. Fitz and Simmons are lab techs, not fully trained field agents, meaning they are likely to resist the bureaucratic system of SHIELD to an extent. Finally, there's Coulson himself, with his belief that getting things done should come before "the red tape". Fury suspected that the SHIELD organization had been compromised, so he created a team that would work outside of that organization, just in case he turned out to be right.
In "Turn, Turn, Turn", Simmons, who's a Bad Liar that likes to follow the rules because it "makes [her] feel nice", has to learn to lie and break the rules repeatedly to keep herself and others safe. Meanwhile Fitz, who's a Cowardly Lion that wants to avoid battle whenever possible, has to stand up to a HYDRA agent he thinks is going to torture him and has to take out another in what is almost certainly his first time killing anyone.
After "Turn, Turn, Turn", the reason for May's constant distrust of Skye becomes clear. She built the team (by giving Fury a list of roles she needed, which he translated into team parameters to give to Coulson) in case he Came Back Wrong. Ward to physically take him down, Simmons to fix his body, and Fitz to operate the machine that would fix his mind. Not only is Skye an outsider, but she's a disturbingly clever hacker who hates secrets and feels a strong bond with Coulson. If anyone could figure out the secrets behind Coulson's resurrection and bring the whole house of cards tumbling down, it would be her.
Looking back to Agent Garrett beating Ian Quinn up and gleefully telling him that he's been abandoned by the Clairvoyant for his failures... He's actually saying "You Have Failed Me".
One-Man Army though he is, one might be tempted to question how Ward came out of his 1 vs. 12 fight with only superficial injuries, especially since he was getting kicked around rather thoroughly at one point. The Reveal that Ward is a HYDRA agent answers the question: The whole thing was most likely a show improvised for Skye's benefit. Ward had to keep pretending he was a loyal SHIELD agent, so when he started attacking his fellow HYDRA operatives, they just rolled with it. It was never as brutal a fight as it appeared.
Where would Centipede get all the Super Serum components for their Super Soldier serum? SHIELD knew and studied them and probably had access to Extremis and Gamma rays, etc. Garrett had access to these components being a HYDRA agent within SHIELD.
Centipede's name. In-universe, it's mostly meaningless, being just a reference to the incidental shape of the device that injects soldiers with the serum. However, from a meta perspective, it makes perfect sense. It's a subset of HYDRA. While HYDRA's motto is currently "Cut off one head and two more will take its place," it's also been "limb" before. A centipede has lots of limbs. HYDRA has had a lot of time to grow...
This one's a tie-in to Captain America: The Winter Soldier. Remember how HYDRA says that if you cut off one head, two more take its place"? Consider that in the AoS tie-in episode, Garrett and Ward take over now that Pierce is dead. Two taking the place of one.
Erik Selvig's comment in the first Thor movie, about Agents of SHIELD confiscating their research like "jack-booted thugs" takes on a whole new level of meaning after events in the episodes surrounding and including the second Captain America movie.
Where did the security team get their Night-Night Gun-like grenades? Ward had access to the research, he then passed it to Garret, who used it to attempt to protect Ian Quinn. This is implicitly confirmed by the Cyber Tech recruiters in "Ragtag", where they mention they've seen ICER bullets before and turned them into aerosol grenades.
When the team infiltrate Quinn's Italian mansion, Coulson is packing real heat, while Ward is using twin Night-Night pistols, a non-lethal weapon. Who else but the HYDRA mole/Clairvoyant lackey would want to ensure that as many people affiliated with Quinn and Centipede are only temporarily put out of action?
With the revelations that SHIELD is infested with HYDRA operatives, including Ward and Garrett and that Nick Fury had to fake his death by assassination to fight them, coupled with the fact that the mytholgical Hydra was a serpent, it seems that Samuel L. Jackson is once again dealing with Snakes on a Plane.
Coulson seemed to find the room that held the GH325 drug rather quickly without any false turns. The reveal in "Nothing Personal" that Coulson was actually the Supervisor of Project T.A.H.I.T.I. now sheds light on this. Even though his memories of what happened to him were altered, on some level he still remembered his way around the facility from before his death.
One of the soldiers that they shoot seems to recognize Coulson. But why would he recognize Coulson if Coulson was only brought there after he was dead? Because the soldier worked for Coulson before Coulson quit the project. It also explains the soldier's "Then you know about the countdown." A random patient wouldn't know about it—but the director of the project would.
This explains why they got so agitated when they realized Coulson didn't know the response to the question "How was the drive from Istanbul?" He was in charge of the project, so he should know the call-sign. This was the first sign that something was off.
It is absolute genius that the team is hit so hard by Ward's betrayal, since Ward is the one member of the team that has had a bonding episode with everyone else on the team: he bonded with Simmons in "F.Z.Z.T", Fitz in "The Hub", May in "The Well"(and well as their, erm, extra-curricular activities), and his entire main character arc revolves around his bonding with Skye (and by extension Coulson). Ward is the one member of the team that had proven himself to everyone else on the team on a personal level, and basically carved a niche for himself as the reliable one. Ward being HYDRA basically yanked the safety net from underneath the entire team, they basically built him up to bring the rest down.
Quinn shot Skye in the stomach in T.R.A.C.K.S. to ensure that she would be in a critical condition. Considering that Garrett was slowly dying from organ failure due to an IED blast causing critical damage near his intestines, this was probably an additional way to make sure that whatever saved Coulson from death could save him from organ failure and the accompanying issues (likely sepsis or septic shock).
Why can Garrett "feel the universe"? Because he's experiencing the negative mental effects that made Coulson want to shut down TAHITI in the first place.
Garrett declaring that he and Coulson are "blood brothers" is essentially laughed off by the latter and Nick Fury as being more crazy talk. However, as we see in The Tag, Garrett just might be not too far off the mark with that statement.
At the time, it seemed really stupid that Ward allowed Lorelei to get close enough to touch him instead of shooting her when he had the chance, but then consider his relationship with Garrett. As Skye points out in the finale, Ward is not as strong-willed as he presented himself to be at the time, so mere proximity to Lorelei could have been affecting him.
A meta example from the season finale. Garrett getting Killed Off for Real by Coulson is not just a Crowning Moment of Funny, it's also an audience-satisfying bit of thematic sense. After all, Coulson and Garrett had been long-time friends and comrades, with numerous escapades together; having Deathlok kill Garrett denies Coulson the closure needed to resolve Garrett's betrayal. Bringing back Garrett for a villainous Crowning Moment of Awesome, only for Coulson to obliterate him in the most trivial way possible, is a thematic Curb-Stomp Battle for Coulson.
Ward mouthing off about how "someone really wanted our initials to spell 'shield'" in the Pilot takes on a new significance after The Reveal that he's actually been The Mole for HYDRA the whole time. He was asked what it meant to be a SHIELD agent and what was his response? He snarked about it to the agent who asked him. A sign that his belief in the SHIELD cause isn't as true as he pretends it is.
Young Ward having issues killing the dog Garrett left him with isn't just a literal Pet the Dog moment. It's an insight into Ward's true personality. Think about the essential personality traits of a dog: They're fiercely loyal to their masters, but they'll become listless and sad when they're not around. In short, they're nothing without their masters. Is Ward not the same way with his master, Garrett? Notice how, when Ward has no mission and no orders, he just seems lost. In some ways, his personality is more dog-like than human-like. No wonder he had trouble pulling the trigger.
In the pilot episode, one factor that contributes to Coulson recruiting Skye onto his team is that she discovers Centipede's involvement in Mike Peterson's powers before SHIELD does. With Coulson emphasizing how rare it is that SHIELD doesn't know that piece of intelligence but a random hacker does, it initially feel out of place and maybe just a weird way to paint Skye as an effective addition to the team. The reveal that HYDRA is secretly in SHIELD, and that Centipede is one of its projects, makes it easier to understand why SHIELD didn't know about them. It is reasonable to assume that HYDRA could cover up their projects and activity with the right people monitoring and covering up any leaks.
Coulson says that the damage to Fitz's brain is too severe and that Fitz will probably never recover. But the conversations Fitz has with his imaginary version of Simmons where she reminds him to take his medication and helps him with words he can't immediately recall show that Fitz's brain has created a way to deal with the trauma and work around the damage, meaning that his knowledge is still there, it's just that he can't directly access it.
The quinjet Triplett and Skye hijack cloaks itself but it still casts a shadow because the technology simply projects an artificial image on top of its body.
Remember that tech-disrupting bracelet Skye had in season 1? The wristband she uses to track her heart-rate as she kills someone for the first time in Season 2 is a call-back to that, except it shows how she's grown.
Hunter's response to finding out his ex-wife vouched for him to join SHIELD—an appalled "Why would you do that?!"—seems at first like just another level of abrasiveness. But as of "The Things We Bury" it makes more sense: he's secretly terrified that as a super-spy she has ulterior motives for everything and is never being honest, which is why they broke up in the first place.
Why did The Doctor have that 'You're Insane' moment with Whitehall? He wasn't calling Whitehall's GOALS insane. He was accussing Whitehall of being a bad scientist, a much more cutting insult.
When meeting with Whitehall, The Doctor comments that "it's always good to look your enemy right in the eye", likely referencing his confrontation with Coulson. However, it's more likely he's pretty much referring to staring down Whitehall, the man responsible for killing his wife.
The Doctor's story about the aliens coming to end the world was more than just him correcting Whitehall about a legend, it was another insult directed towards the man. Whitehall shows an intense fixation on these legends and being corrected on them for even a minor point would likely make him infuriated on the inside, which The Doctor would enjoy.
When Bobbi interrogates Bakshi, she references borderline personality disorder, by way of explaining his unreasonable commitment to Whitehall. This also illuminates Ward's psychology and motives, grounding his character in something more concrete than "Someone who betrays people a lot." It's also consistent with his behavior towards Skye since Garrett was killed.
Ward's behavior towards Skye comes across as a stalker, but when you look at what Garrett put him through, you realize it's more than that. Garrett constantly abused a Ward and forced him to suppress his emotions, and before that he was at the tender mercies of his mother and older brother. It's likely that he has never experienced a healthy relationship with another person, so he has no idea how to interact with others positively. Acting like a Stalker with a Crush is the only way he can express himself to someone he's attracted to.
Trip's death gains new meaning when you remember that his grandfather was a Howling Commando. His death is symbolic of the death of the old guard that was SHIELD.
The Doctor's violent mood swings make a lot more sense when you realize his name is Cal and his daughter is an Inhuman named Daisy. For those needing more explanation, this is confirmation that he's the MCU version of Calvin Zabbo, AKA Mister Hyde.
Skye starts off as a computer hacker, and in the second season we find out that she's the MCU version of Daisy Johnson. A little known fact about Daisy is that she was originally modelled after Kate Libby/Acid Burn, a character from the cyberpunk film Hackers (three guesses as to what Acid Burn did in that film). Pretty smart forshadowing there, writers.
Was it reallyOdin who sent Sif to recapture Lorelei? We already know that Loki was pretending to be him at the end ofThor: The Dark World. Sending Sif alone with specific orders to bring in alive a foe she had personal tragic history with? Totally Loki-style trolling. However, considering Lorelei's powers, could it be the next step in Loki's own story? Furthermore, Sif would most likely have to give a full report on what transpired on Earth. Including the fact that Coulson is alive. Even if she tried to keep it from Loki-Odin, he would either a) pull rank and order her to tell the whole truth as her King or b) Ask Heimdall about it. In either scenario, Loki now knows that Coulson is alive, and will be very curious about how he managed to achieve that feat.
Another one involving Loki: in The Avengers he tells Romanoff that members of her organisation 'lie and kill, in the service of liars and killers'. With HYDRA coming out of the shadows, and having infiltrated SHIELD thoroughly, right up to its highest echelons, he was dead on the money.
Coulson's flashback in The Magical Place shows that he was awake through all of the surgeries they put him through, and he was in excruciating pain the whole time. What they don't show is him moving at all, which means he was probably being routinely injected with strong paralytic drugs. Imagine being in that kind of pain and feeling completely trapped because you can't even move.
In "Seeds", we learn that when Skye was an infant, someone had every citizen of a small village in China killed to get to her. Horrible on its own, but it also raises the question: What exactly can Skye do that someone would expend that kind of effort to get? Answer: Given the kind of people who typically resort to such methods, probably nothing good. Also, how much of it is metaphorical? The people looking for Skye were monsters, her parents; "monsters" since they slaughtered a whole village looking for their daughter, or "Monsters" as in Chitauri/Kree/Skrull/etc.? Exactly how human is Skye?
Remember how Ward justified his kill count to Skye? He called the people he killed "terrible people". If he really is loyal to HYDRA, then who do you suppose he considers "terrible people?"
Asgard doesn't know about HYDRA. The next time they need to show up on Midgard, they'd be looking for SHIELD, knowing them to be allies. Which means that Asgardians could walk right into HYDRA without any suspicion. And to make matters worse, thanks to Lorelei getting control over Ward, she could know everything about HYDRA's presence...which then means that, as his prisoner, Loki might know as well.
At the end of "Turn Turn Turn" Coulson and Hand discuss how in the fall out, HYDRA has claimed at least 2 of SHIELDS bases, and an untold number of others. What happens if Hydra gets their hands on a key base, like The Sandbox where they store all the 0-8-4's, or The Fridge, where they keep high security prisoners, like Blonsky? As of Providence, this has born fruit...and got a whole lot worse. Turns out not only are prisoners stored at the Fridge, so are all the 0-8-4's that Fury claimed were sent off on the Slingshot.
Combination of this and Fridge Brilliance: Regarding the episode "The Bridge", it's been noted that Ward was really stupid for taking a sniper position that prevented him from seeing the exchange, making him functionally useless if it went south. Given the reveal that Ward is a HYDRA agent and the fact that Centipede is a HYDRA project, it's entirely likely that Ward knew what would happen with the exchange and put himself out of the way on purpose. He allowed Coulson to be captured, all the while playing the role of a loyal SHIELD agent.
What happened to Mike's sister? When Centipede showed up to take Ace, she didn't just agree and hand him over, so there's a high chance she was killed, and worse, would have lay there until someone went into the house and found her, and considering her house appears to be a farm in the middle of nowhere, that could have taken quite a while. Another option which isn't really better: The SHIELD agents guarding her and Ace were Hydra agents, and simply told her they had orders to take the kid to see his dad. She would have handed Ace over to them completely trusting them.
With the revelation of who was in charge of T.A.H.I.T.I., consider the two guards at the T.A.H.I.T.I. base. Their old, friendly boss comes over acting like he doesn't know the procedure. Either they knew what had been done to him or not. To them, they were either killed by an imposter desecrating the image of their old boss, or they knew they were being killed by their boss who didn't know who they were. Given how Coulson treats agents under him, those two were likely his friends. Either way, horrifying.
One of the flashbacks Coulson had when remembering his resurrection was repeatedly saying "Please let me die" while getting his memory rewritten. "Nothing Personal" shows Coulson was the supervisor on the T.A.H.I.T.I. and described massive risks in psychological breakdowns observed in their test subjects. The issues could be minimized and possibly resolved through memory rewriting, but success was not replicable enough to have T.A.H.I.T.I. be considered a reliable solution to overcoming death. It's harder to tell now if Coulson's begging for death was due to the trauma of dying and getting resurrected, or because he knew what was happening and what possible side effects he would expect from the T.A.H.I.T.I. research being used on him.
In "Yes Men," Ward continues to attack May and attempts to shoot her after Sif subdues Lorelei. Seems like bad editing at first, right? That was his first attempt to eliminate May. When it fails, then he drops his gun and pretends to have just recovered from the effects of Lorelei's mind control.
The revelation that Ward works for HYDRA makes the events of "Yes Men" an even bigger threat than previously known. Though her control of Ward, Lorelai could have become aware of HYDRA’s existence. She could have worked her way up the HYDRA hierarchy and gained control of the organization, and through it, control of SHIELD. Lorelai was actually closer than anyone thought to taking control of the planet.
In "Providence", Ward encounters the Berserker Staff again in the Fridge raid. This time, although he's wearing gloves, he's got more of a satisfied, pleased look on his face, in comparison to the wariness and dislike of the Staff he displayed when allied with Team Coulson. Another indication that Ward is one screwed-up son of a bitch.
Phil Coulson is one of the most powerful non-heroes in the MCU right now. And the side effects from TAHITI are starting to kick in. He's utterly calm when writing the alien language on the wall... with a knife. He knows what the other side effects are. Eventually, he's going to be suffering from the catatonia, the delusions, the inability to communicate, and who knows what could be effected because he couldn't read a memo, couldn't write a note, or hallucination!Loki decides now would be the best time to recreate stabbing him.
So Project TAHITI was originally intended to revive fallen Avengers in the event of their deaths? Given the way ordinary human test subjects reacted to the treatment (going insane from the process)), just imagine how someone like Bruce Banner might have reacted (or heaven forbid, Thor, whose physiology is vastly different from a human's.) It's definitely for the best that the project was scrapped. This becomes even wrose with The Reveal that the TAHITI drug was compelling those who were injected with it to recreate the image of an unidentified city. Imagine how, say, The Hulk might have accomplished this. The whole city of New York could very well have become his medium.
When the movie had a Bittersweet Ending, with Agent Hill and Agent 13 seemingly being able to fit into a post-SHIELD civilian life, here it turns out that in the case for Hill, even though she has renounced SHIELD, was instrumental in its downfall, and was in fact on the top of Hydra's kill list, she remains under suspicion by the US government and is under constant surveillance. It was even hinted at by her phone call to Pepper that the only reason why she hasn't been arrested was because Stark is protecting her with his team of lawyers.
With the fall of SHIELD, not only are thousands of non-HYDRA-affiliated employees now not only out of a job, even those that are morally upright loyalists that have resisted against HYDRA's attempted takeover (such as Team Coulson) are being hunted down by the US government as terrorists. Even non-combatants such Fitz Simmons and Skye were threatened by Col. Talbot with imprisonment for their affiliation with S.H.I.E.L.D. Think about how it must be like for all the other S.H.I.E.L.D agents still out there. One day, at the SHIELD base that you were working in, half of your colleagues who you have always thought were your friends, suddenly turns out to be working for a neo-Nazi organization and you were forced to kill them in self defense. Once the dust settles, you discovered that you have unwittingly helped further a plot to kill literally millions of people, and SHIELD has been declared a terrorist organization. You now find yourself sitting at a base full of advance reversed engineered alien technology with military applications, all your funding and support has been cut off, your own government which you have loyally served is hunting you down like a criminal even though you have done nothing wrong yourself, and said neo-Nazi organization is still fully operational and is threatening to raid your base at any second.... So, what choice do you realistically have? Try to sell whatever you can to Oscorp or The Ten Rings simply to get enough to survive and make a run for it? Apply for political asylum in Latveria in exchange for your services? We are looking at the same level of chaos that were cause by the fall of the USSR taken Up to Eleven. With all this technology and manpower being up for grabs by unscrupulous corporations, despotic governments, and terrorist groups worldwide. With SHIELD collapsed, who's going to stop them?
The outcome for any agents who are killed? They're put in unmarked graves, and don't get funerals. Chances are that their friends and family don't even know that they're dead.
The TAHITI drug caused those who were injected to experience the GH alien's last memories, including its frantic desire to get to an unidentified city, which is why they were compelled to draw the carvings (which turned out to be a blueprint of said city) using any medium they could find. The emotional states of the injected would suggest that the alien was in some kind of panic just before dying, which raises two questions: 1) What happened to make a creature like that so freaked out? and 2) Is whatever caused it to be so afraid still a threat in the present day?
When Whitehall is torturing Raina he comments that he once operated on a woman for a week and that "the hard part is staying awake." Later, it is revealed in The Things We Bury that he operated on and ultimately killed Skye's mother to gain back the youth he had lost.