- Building off of what happened in Captain America: The Winter Soldier, the show's second half of the first season, and the second season, explore the after effects of the film. Primarily, a big government agency can't just suffer a major scandal like the S.H.I.E.L.D./HYDRA infiltration situation without having everyone, regardless of their involvement, coming under scrutiny. Similarly, you can't just dissolve an entire spy organisation the size of SHIELD without the remaining resources now being up for grabs, both by the traitorous HYDRA members and the remaining agents. And even if the former agents aren't HYDRA, it doesn't mean they're going to be doing anything other than looking out for themselves.
- Before that, there was the Thor: The Dark World tie-in that explored how the public would react to Norse gods showing up and smashing shit up. They don't react well, to say the least, and anti-Asgardian hate groups sprout up trying to find a way to counter their presence. Ironically, it's not too dissimilar to SHIELD's reaction to the first time Thor showed up, resulting in them trying to make WMDs that could take them on if needed.
- Skye had feelings for Ward, until she learned that he was really a member of HYDRA. Those feelings disappeared immediately.
- Skye is trained by Ward to disarm someone, which she learns to do quickly. When she's forced to use it later, however, she ends up running from the conflict as, while she can disarm someone, she can't actually use the gun yet, nor would she stand a chance at fighting without one, or even have the mental capability to shoot someone in the first place as it is.
- After May learned from Lorelei that Ward had feelings for Skye, she ended their Friends with Benefits deal immediately.
- Ward thought he could make amends with Coulson by giving up information about HYDRA. Coulson pointed out that Ward could never make amends for murdering loyal SHIELD agents and trying to murder his friends, before handing Ward over to the latter's brother (an influential US senator) as a bargaining chip. Similarly, while it's left ambiguous whether Ward was telling the truth about his brother's abuse, the team themselves refuse to believe his claims, as is to be expected after all the time he spent ruthlessly and consummately lying to them. Not only that, if you commit multiple murders and acts of terrorism by your own free will, it doesn't matter if you had a tragic childhood, or you feel real bad about it. Like most criminals or terrorists who act of their own choosing, you get punished accordingly and fittingly.
- In the middle of Season 2, Ward kidnaps Daisy at gunpoint, brings her to her father, things go south, and he tries to get in Daisy's good books by freeing. The normal cliche is for them to reluctantly work together to get out, then she either captures him, kills him, or he gets away so he can finish off the season. Instead, Daisy immediately grabs a gun, shoots him in the back four times, and leaves him for dead.
- On the flipside, the team's hatred for Ward and unwillingness to even be civil towards him come back to bite them in the ass as he consolidates HYDRA's resources and decides to use them to make Team Coulson's lives as miserable as possible.
- The team's reaction to Ward's betrayal is especially realistic. Anger and rage are expected responses. A tragic backstory does not erase harm done and broken trust. A normal human response to a person willingly betraying and trying to kill them (in Fitz's case, leading to neurological damage) is open hostility, especially when said person takes no blame for pain caused.
- Ironically, Ward's failure at being a genuine threat as the head of HYDRA is also an example of reality ensuing. While Ward created his little group as revenge for Kara dying (ignoring that it was by his action and his hands), his HYDRA cell gets dismantled by three people and Ward only escapes death due to Hunter's mistake. Ward may be a highly skilled and charismatic operative, but those qualities don't automatically make him a competent leader. To hammer the point home, Ward eventually realizes this, and settles on becoming the second-in-command for the season's real villain, Gideon Malick.
- Hunter's constant complaining about his ex-wife results in this when we meet her. Generally, if you can't stop complaining about her, to the point your co-workers react with annoyance when you bring her up, especially when they know that the ex is both a nice person and not nearly as bitter as you, you end up being the one who looks like the unreasonable ex. The end result? Everyone takes Bobbi's side.
- Daniel Whitehall is an incredibly dangerous man as the leader of HYDRA, having brainwashed countless people, conducted horrific experiments in the past and present, and vivisected Daisy's mother to steal her rejuvenating abilities. He still goes down immediately to two bullets in the back when Coulson gets the drop on him.
- Hunter and Bobbi are let go by Coulson when they decide to break cover in a mission to Russia to defend a Russian dignitary from being assassinated, and the dignitary becomes furious that SHIELD (an underground espionage organization, formerly American, with covert American support) is doing espionage in Russian soil. Even if things are more complicated than that, in the end it does no good for a spy group to have public enemies on their line-up.
- Joey has powerful Inhuman abilities that can be quite dangerous in combat and protect him and his allies from attack, but he's no soldier and he has very little spy training, and is totally unused to the prospect of taking human life. When forced to kill Lucio to save his teammates, even though it was in self-defense, he reacts poorly. Likewise, when the truth that HIVE has infected one of the Secret Warriors comes out, he decides he's had enough and calls it quits on S.H.I.E.L.D.
- Daisy has the ability to generate powerful vibrations from her hands, which have the same effect as a small, localized earthquake. The constant use of this ability begins to cause internal damage, and in Season 4, a running plot point is that she has to take special drugs to help heal and regrow her shattered bones.
- When Ghost Rider is introduced in Season 4, Daisy manages to track him down rather quickly, as his insanely Cool Car isn't exactly common in the low-income L.A. neighborhood where he lives.
- In "Self Control", LMD May sets off a huge bomb in the Playground to let the agents escape LMD Coulson while there were still others inside the base. Naturally, people are left in critical condition after such an explosion, with broken bones and third degree burns, as revealed in "The Return".
- Having spent months drugged into unconsciousness during season 4, when May regains consciousness in "Farewell, Cruel World!", she's too weak to even stand, let alone walk.
- In season 5's "The Real Deal," the team tries to reconcile the idea of people's worst fears being made manifest with the discovery of a forest. Turns out that if someone's been raised their entire lives in a sterile, rock-hewn tunnel system, they're going to end up with some serious agoraphobia.
- In "Inside Voices", Ruby proves herself to be vastly superior to Carl Creel in terms of fighting skill, easily dodging almost everyone of his blows while getting off some strong hits of her own...and it does almost nothing to him, because no matter how skilled and acrobatic a fighter she is, a 90-pound girl fighting with punches and kicks is going to have negligible effect on a fully grown man who's twice her size and built like a freight train, and that's without taking his Elemental Shapeshifter abilities into account.
- In "The Force of Gravity", Coulson and May are trapped inside a prison cell when Deke suddenly bursts in to rescue them. Except instead of being all tall-standing, confident and badass like any of the other agents, he's hunched over and panting in exhaustion because he's not used to intense fighting for long periods of time and is so tired he can barely stand up after exerting himself beating up some Remorath.
Reality Ensues / Agents of S.H.I.E.L.D.