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 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 the 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.
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."
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?
After the fact, Ward even lampshades how unusual it is to see May lose her cool like that. When she stops being The Stoic, you know it's serious.
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.