At the end of the pilot episode, when you realize that the shot was not a bullet but the cure that the team managed to come up with in time. It then cuts to Mike Peterson's son out on a idyllic farm in the countryside, and Coulson and Skye discussing Mike's recovery.
Coulson breaking his cool to demand that his team find a way to cure Mike, and sympathizing with Mike about how it feels to be an ordinary man in a world full of superheroes.
We discover that while Ward may come across as a No Social SkillsJerkass, he reveals he dearly loves his grandmother. Also a Funny Moment, given how the normally stoic Ward acts like a little kid for a few moments.
Skye insisting to Mike that S.H.I.E.L.D. can help him. That's a lot of faith to put in a group that she openly distrusts.
It took more than a few years, and he can't be here to see it, but Howard Stark finally gave the world flying cars. Man's dead, and still taking us to school.
Camilla mocks Coulson for downgrading from leading hundreds of agents to a team of six. Coulson answers with a Badass Boast saying that his team will defeat Camilla and her soldiers. They're that good.
The team relaxing and watching the rocket carrying the 0-8-4 device blasting off into space. Grant even gives Leo a friendly clap on the back. Even if it's revealed that Skye's acting as The Mole for the Rising Tide, it's still a nice moment.
Quinn reminds Skye that SHIELD is everything she's against and that they're Big Brother. This is her response, which borrows a bit from Grant's "Defining Moment" story:
May being so concerned for Coulson's safety that despite her reasons not to (which are implied to be strong reasons not to) she immediately asks to be put into field work on his return so he doesn't have to risk himself.
Coulson's almost fatherly concern for Akela.
Particular mention to his realization that she's being forced to do all these villainous things. The way his face lights up knowing she didn't willingly betray him...
Skye says that Coulson is a great judge of character and thanking him for being the first person to value her in a long time. Because of this, she says she trusts him when he says that Akela deserves a second chance even though May disagrees.
It's small, but Skye referring to May and Coulson as Mom and Dad.
When Coulson and Ward visit the hotel Akela's staying at, the receptionist tells them how Akela told her to go to the doctor, where she was diagnosed with a tumor. Akela spotted it with her implant, and more than likely saved the woman's life.
When Ward, pretending to be Akela, completes her mission, her handler tells her "Good luck" when "she" has to escape. It's heartwarming in hindsight once you realize that her handler was a prisoner just like Akela. Even though she didn't know it, her handler did actually give a damn about her.
Akela finally being able to sleep at the end without someone watching her every move.
Girl in the Flower Dress
Skye and Ward playing a friendly game of Battleship. She even gets him to finally smile!
Coulson making sure Agent Quan's family gets some money.
Coulson agreeing not to cut Skye loose after finding out that she joined the team in order to search for her parents. He still clearly doesn't trust her entirely, but he agrees to help nonetheless.
It's especially notable that once the truth is revealed, Coulson immediately goes from anger and disappointment to sympathy and understanding. Despite all that's happened, he's still willing to give Skye a second chance.
While the rest of the team is either angry or upset at Skye for her betrayal, Simmons is the only one who understands what she did, and still considers her the team's friend.
Fitz: Why would Skye do this to us? For him. Thought she was our friend. Simmons: I think she is, Fitz. He's just obviously more than that. Fitz: Yeah, but we've been through so much together, and she didn't even tell us that she has a guy. Simmons: Well, who knows what they've been through together.
Fitz being totally understanding of Skye, apparently having already forgiven her. To the point of awkward flirting.
Coulson comforting the volunteer firefighter after the team realizes the latter is infected with an alien virus, and will die in a few minutes. Coulson tells him that he has died already, and spent a few moments in the afterlife. He also assures the fireman that it's beautiful.
Fitz's unwavering support while helping Simmons cure her own infection. Including being totally willing to parachute after her and cure her in midair after she jumps out of the bus.
Including jumping into quarantine with her, despite not even wanting to be in the same room as a dead body. When Fitz enters the quarantine with the Chitauri helmet:
Simmons: No, uh, You can't be in here. Fitz: Too late, it's done. Just try and do your best to keep your hands off me yeah?
Before that, how he's making jokes and trying to cheer her up behind the glass doors.
Even before that, there's a moment when Fitz is just sat on the floor with her on the other side of the glass. He doesn't say anything; he doesn't need to. He knows that just sitting next to her is enough.
Ward pretending not to notice how heavy the gun is the second time, to play along with Fitz and Simmons.
Once everything's said and done, Skye says nothing. She just hugs Simmons as hard as she can.
Simmons thanking Fitz for staying with her and saving her, complete with a kiss on the cheek.
Simmons: You're the hero.
Coulson finally confesses to May that he's convinced he Came Back Wrong. She tells him dying is traumatic, and he shouldn't expect to be the same as before, but that doesn't mean anything's wrong with him.
Skye hugs Coulson after he finds out what the redacted document from her orphanage said.
The entire conversation between Fitz and Simmons before he goes on the mission. And the sandwich.
At the end, Fitz doesn't have the heart to tell Simmons he didn't eat the sandwich, so just tells her it was delicious.
Fitz and Ward realizing Coulson told both of them to take care of the other.
May leading the girls to the Bus to extract Ward and Fitz. "Let's go get our boys back."
Coulson joining them.
Skye is willing to give up what she knows might be her only chance to look at the files about her past, to keep looking for info to help Ward and Fitz, when she realizes she won't have time to do both.
Of all people, Victoria Hand is the reason for one. Coulson confronts her earlier in the episode when he discovers that Fitz and Grant do not have an extraction team. Later, when Agent Sitwell asks why she did not assign an extraction team, she says that all their resources were being used elsewhere, and that they didn't need an extraction team: she knew Coulson's team would rescue them anyway.
Randolph to Simmons after being revived: "You're the most beautiful thing I've seen in a thousand years."
Simmons finally mustering the courage to talk to her parents after all the drama since "FZZT."
May's silent invitation to Ward to share some wine in her room after the Berserker Staff brought out their worst pain.
Also earlier, after using two parts of the staff to fight off assailants, reinforcements arrive. Ward wearily reaches for the pieces again when May stops him and uses them in his place.
Grant, who has previously been accused of having no people skills, helping Jemma with her fear of heights and her acknowledgement of her own awareness of him trying to trick her and him assuring her that if she falls, he'll catch her. It takes on more meaning when you remember how he caught her in F.Z.Z.T.
During the flashback to Ward's childhood, where Ward is told if he helps his brother out of the well he'll be thrown in too. What does Ward do? Help him out anyway, all whilst visibly terrified.
Skye's genuine concern for Ward while the staff is affecting him, especially given how terrified she must be of him in that moment. (Imagine how you would feel if your normally calm, collected co-worker started losing his cool like that.)
Both Skye and Coulson are confident that they can help May go back to being the warmer, kinder person she once was even if she doesn't.
Skye goes to keep May company in the cockpit. Even though May once said she enjoys the solitude of the cockpit, she doesn't kick Skye out.
Skye comforting Hannah, telling her that, even though she's not religious, her preferred interpretation of God is that "God is love" and therefore would not punish Hannah in the way she fears.
Towards the end of the episode, Coulson tells Skye that she has the potential to do this kind of thing (finding people like Hannah and comforting them) all the time.
While it was a little creepy, there is something heartwarming about the villain's motives; he wanted to protect Hannah because he loves her.
In the stinger, May pulls a prank on Fitz, showing whatever traumatic experience she had with the Gifted girl didn't completely destroy the person she used to be.
In that same stinger, we see that the Team (minus May and Fitz) is enjoying a game of Scrabble together, perhaps showing even more of the closeness that Coulson had hoped for when he assembled them.
Coulson's little chat with Ward about The Cellist. It's clear he was quite taken with her and losing her due to his "death" wasn't easy.
Ward, Fitz, and Simmons are uncomfortable with Mike joining the team as the last time they met, Ward shot him with a gun Fitz and Simmons designed. Mike reassures them by thanking them for tranqing him instead of killing him. He also thanks them because the tranquilizer helped stabilize the serum, preventing any more explosions.
The Magical Place
The real reason May told Hand that Skye should be kicked off The Bus. The girl works better when she doesn't have by-the-book SHIELD agents breathing down her neck. Despite how harsh and cold she seemed, she was counting on Skye to find Coulson, which means she values Skye's skills and trusts her to do a good job.
The little look they give each other at the end says it all. Skye seemed to have understood May's intention and realize she doesn't really hate her, while May seems geniunely flattered Skye choose to model her "Shield agent" self after her.
Nick Fury "moved Heaven and Earth" to keep Coulson alive after Loki stabbed him. That's how important "his one good eye" is to him.
Becomes some Fridge Horror after "T.A.H.I.T.I." when we learn exactly what "moving Heaven and Earth" meant: Fury captured a half-dead member of an unidentified alien race and had it kept on life support so as to continue pumping a healing drug out of it's body. This was used to save Coulson. Judging by the look on Coulson's face when he discovers it and his subsequent rush to stop it from being used on Skye, it's a procedure that he would not have knowingly permitted Fury to use on him.
Coulson reuniting with his team; major feels from everybody but especially Skye.
Coulson rewarding Skye for saving him by removing her Walking Techbane bracelet.
After two SHIELD agents lose their entire team to recover an 0-8-4 that was Skye as a baby, they set up a hidden protocol to keep her safe throughout her life.
Coulson and May talk to one of the SHIELD agents who found Skye as a baby. After all he's been through, his top concern is whether the baby is okay.
Fitz bonds with Donnie, a loner student at the SHIELD Academy, by helping him improve a high-power battery he's working on. It turns out badly later on, but it's still a nice scene.
In the same scene, when Fitz is commiserating with Donnie about being lonely at the academy, he mentions how much better everything got for him once he became friends with Simmons.
Couslon holding Skye's hand as The Bus was descending down the eye of the storm.
Skye goes to the SHIELD Academy memorial wall to honor the agents who died protecting her as a baby. It becomes more heartwarming when you consider something she said earlier in this episode. Even at this point she feels an outsider because she didn't go to the Academy and so she isn't part of SHIELD's history and tradition. Now, she's learned that her original foster parents were SHIELD agents.
Skye tells Ward that she feels like she cheated by getting into SHIELD by hacking their system. Ward gives this as his response:
Ward: All you need to join is dedication to the greater good. Coulson saw that in you the moment he met you.
The Mythology Gag of Skye reading off Bucky Barnes's name at the Wall of Honor also manages to combine moments of Heartwarming, Tear Jerker, and Funny: heartwarming that Bucky has been honored and remembered, tearjerker considering the upcoming Captain America: The Winter Soldier, and funny as another instance of Skye's fangirl tendencies towards the superhero universe.
Simmons sees Fitz and Skye fighting off a man with a grenade. Simmons immediately grabs the guy and holds their bodies together to contain the blast. Granted, it was a nonlethal tranquilizer grenade, but the fact remains that Simmons' first instinct was to protect her friends at the cost of her own life.
Not to mention Fitz' steps to care for her while she's still unconscious/paralyzed: helping move her body into a comfortable position, making sure she has a weapon to defend herself with when she wakes up, and gently closing her eyelids.
After Simmons has finished stabilizing a dying Skye, Fitz holds her while she quietly cries in the supply closet.
When a doctor tells the team there's nothing that can be done to save Skye and they should call her family, Coulson looks over the team and says "We're her family."
What the team is willing to do for Skye. Period.
May showing that despite her initial dismissiveness towards Skye, she's come to care for her. See the beatdown she lays on Quinn in the interrogation room for proof.
Quinn: You can't! May: Why? Because you're defenseless? Like she was?
Simmons saying that even though she and Skye are "nothing alike", she "can't imagine her life without her". More proof that Skye and Simmons are great friends.
Simmons fussing over Skye while she's in the hospital bed. She acts like a mother hen, or in Skye's words "a prison warden". Then Ward comes by and they share a sweet moment.
Sif telling Coulson that Thor considers him a good friend and was very upset about his death.
Coulson tells her he feels the same way, which is why he wants to tell Thor he's alive himself.
Just look at at the way May smiles through all her interactions with Sif. In particular, she looks happier when the two of them are talking privately and comparing weaponry techniques than she has at any other point in the series. Whatever other issues she has going on, she's a total Fangirl for Asgardian warrior women.
While the scene where Coulson tells Skye about the alien corpse that provided the miracle drug that saved them both is plenty serious, it still counts because he sounds more worried about her than for himself or she is for either of them. Thus, he sounds like an Overprotective Dad.
Skye's reaction, too. She's not upset or blaming him or anything. In fact she's genuinely confused as to why Coulson seems to think she'd have anything but gratitude for saving her. In fact, Skye's whole reaction to the entire situation is basically "I need to get better so I don't have to burden everyone to worry and need to save me like this again."
End of the Beginning
Skye finally officially being accepted as a Shield agent
Coulson: Welcome to SHIELD, Skye.
Agent Blake, a character who appeared to be somewhat callous previously, still offers to get Mike/Deathlok help, even when he has him by the throat.
Just before shit starts to go down, Coulson tells Fitz to get back to the van. It's a small thing, but Coulson knows that not only would Fitz be useless in combat, more importantly he'd be in danger.
Turn, Turn, Turn
When Simmons and Fitz are finally reunited, she runs directly to him and they share a hug of relief.
Ward and Skye's heart-to-heart (ending with something of a Big Damn Kiss) is something of a CMOH for them—especially for shippers of the two. How it jives with the episode's last big "reveal" has yet to be seen....
Raina's "Gift from the Clairyovant" is a new flower dress. Given how evil the guy is, it's awfully thoughtful. The look on Raina's face is comparable to Coulson receiving a gift from Captain America.
Ward is still showing concern for Skye in his HYDRA agent persona, thus his "true" persona. He gave Garrett an earful for calling a hit on her. Then he admits that killing her would difficult for him even if Garrett were to order it.
FitzSimmons almost manage to have a heartwarming moment together when discussing their doubts about Coulson, when Simmons says that despite everything that's happened at least they still have each other. This cheers Fitz up enough to raise the fact that he hopes things won't change (meaning that the two of them will still stay together even without SHIELD keeping them that way) - at which point, Simmons being Simmonsmisses the point completely and, thinking he's talking about the team and the organisation more generally, gently explains "It's too late for that." Fitz's expression makes it pretty clear she's inadvertently killed the moment stone dead.
The Only Light In the Darkness
As part of Koenig's vetting process, he has each agent undergo a polygraph test on steroids. One of the questions places the subject in a scenario where they are trapped on a desert island with a box and asks what the character would find in the box. Fitz's answer, after a bit of beating around the bush, is Simmons.
Ward's attempt to get Fitz to tell Simmons how he feels about her is a weirdly heartwarming Pet the Dog moment. "Weirdly heartwarming" in that he's trying to encourage Fitz to do something about it now, because he's planning on killing them both later. His annoyance when Fitz pretends to have no idea what he's talking about makes his initial attempt to be nice seem quite genuine.
Audrey talking about how when Blackout first attacked her years ago, Coulson was the one that came and tried to comfort her and reassure her that everything would be alright and that SHIELD would take care of everything.
When Audrey is knocked unconscious by Blackout's explosive death, Coulson kneels over her, kisses her forehead, and assures her that he's there and watching over her before vanishing back into the shadows. It's as heartwarming as it is heart breaking.
Alone in the wilderness, on the run from HYDRA and SHIELD, abandoned by one of her closest friends in the world, who does Melinda May call for a ride? Her mother. She may dish out a few gentle reminders about manners, along with what's apparently genetic levels of deadpan snarkery, but she clearly cares for her daughter enough to cross the Canadian border and hijack an unnamed agency's intel to help her.
Doubles as one for May. She left because Coulson couldn't get past her lying to him about his resurrection. Since she doesn't have all the details, she's apparently intent on tracking down one of the few people who do: Maria Hill.
There's something quite comfortably sweet about Maria Hill casually discussing her bad day over the phone with Pepper Potts. Partly because it's maybe the first scene of Hill's in the MCU to break down her stoic persona for a few moments, partly because Pepper manages to play the role of everyone's best friend even when she's not featured on-screen.
Coulson refusing to sell out his team to Talbot.
Fitz and Simmons at the motel pool, telling each other that they aren't HYDRA, just so they could hear it from the other person.
Also at the pool, Coulson giving Skye a candy bar - and in the background, Trip sharing his snacks with Fitz and Simmons. Everyone's had a terrible few days, and they're working with each other on getting over them. Fitz seems to accept, hopefully meaning that Fitz will stop feeling so threatened by Trip's presence in the future.
In an example mixed with Tear Jerker, Hill says that Coulson could join her at Stark Industries, since Stark would more than happily employ him. Coulson turns her down then asks her to pass his greetings along... before remembering that Stark still thinks he's dead.
The reveal of Project T.A.H.I.T.I.'s purpose is one after analysis: Project T.A.H.I.T.I.'s purpose was to revive an Avenger if things came to worst. How is that a heartwarming moment? Cause Coulson was its subject, which means Nick Fury values Coulson as much or more than what he values an Avenger.
Skye calls herself weak for saving Ward. Coulson's response: "You're not weak. You have compassion. That's harder."
May comes to Skye's room to make Skye feel better about what happened with Deathlok and Ward.
Fitz's unshakable faith that Ward is not truly evil and that there is still good in him.
Fitz palling around and generally bonding with Tripplet. Even their failed attempt at a Handshake Substitute has them both grinning at the awkwardness, a telling departure from their non-stop snarking at each other given the slightest excuse in previous episodes.
Coulson telling May how glad he is that she's back. She even smiles at this comment.
When Fitz and Simmons are discussing which Dwarf robot to sneak onto the plane, Fitz nominates Sleepy because "He's our best listener. Apart from you." Simmons looks quietly pleased with the compliment.
Odd example; as Ward has been sulking after Garret nearly had him killed to motivate Skye, he quickly snaps out of it to help Garret get his cybernetics working again, snapping at Raina when she doesn't clear the room like he demands, then muses how its 'been a while' since he had an incident like that, implying that he's spent a lot of time helping Garrett out with his cybernetics. Then later when an EMP shuts them off completely, he's visibly even more worried than he was prior. And, lastly, his initial refusal to kill Buddy, and his clear trouble with dumping FitsSimmons out of the airlock when ordered to kill them.
The Beginning Of The End
"Dad, what are we? We're a team." A wonderful Call Back to the pilot episode.
Fitz and Simmons telling each other just how important they are to each other - Fitz is Simmons' "closest friend", and Simmons is "more than that" to Fitz, though he can't tell her how much more. So he shows her.
Nick Fury responding to Coulson's What the Hell, Hero? speech about T.A.H.I.T.I. being meant for a fallen Avenger with not only the fact that Fury considered Coulson an Avenger, but a true believer in S.H.I.E.L.D.'s founding principle of "protection", and caps it off with entrusting the rebuilding of the agency to Director Coulson.
Skye does this in a Kirk Summation when she tells Ward that Fitz is a hero since he tried to give Ward a chance to explain himself.
There's something oddly touching and beautiful about Simmons's speech about the First Law of Thermodynamics and how it pertains to the afterlife. Nothing is ever destroyed, it just becomes something new.
Fury tells Simmons that she saved Fitz's life. She immediately insists that it was the other way around.
Skye and Simmons' hug when the Bus arrives at their new S.H.I.E.L.D. base. Simmons in particular looks like she really needs it.
In a crossover with a Tear Jerker, Simmons' whole final scene of the season sees her trying to maintain a reassuring smile and take a positive approach to Fitz's condition as she explains it to the others.
After Coulson calls out Nick Fury on subjecting him to a process that could drive him insane, Fury replies that May was on it and told him Coulson was fine. Then, just before leaving, Fury tells May he assumes she'll have Coulson's back as usual, to which she responds, "Of course." It's nice to see that he appreciates what May has done for Coulson, and that Coulson has absolutely forgiven her.
Fury flat out calls Coulson an Avenger. Doubles as a Call Back to The Avengers when Stark lists all the people Loki "pissed off".
When announcing this show and that Coulson would be the lead, the powers that be at Marvel acknowledged that Coulson, through Clark Gregg's portrayal, had become the heart of the MCU.
While promoting the show at Comic Con, Clark Gregg was asked what it was like to be brought back to life and given his own show. His answer was to happily lean over and hug Joss Whedon.