Peggy breaking down and bursting into sobs over her roommate's murdered body.
And later sadly telling Jarvis that she keeps losing people she loves.
Bridge and Tunnel
Thanks to the events of episode 1 Peggy becomes unwilling to get close to people and adopts an I Work Alone mentality. Jarvis has to practically beg Peggy to let him help her and even then it's only after saving her and then telling her that her opinion of Steve is little more than Hero Worship that she begins to accept his help.
The episode also reveals that Jarvis and Stark are hiding something from her, which really isn't going to help her trust issues.
Time and Tide
Though it's minor compared to later events, you've got to feel a little sorry for the woman who got evicted from the Griffith for having a boyfriend stay over, especially since the landlady is so cruel to her.
Peggy having to pretend to be just as useless as most of her co-workers think to get Jarvis out of SSR custody. This also results in her being extremely curt with Angie, putting a serious damper on their friendship.
The reaming out she gets from Thompson is just painful to watch, because we know how capable Peggy is, and she knows, but it's clear to everybody that her actions to save Jarvis have cemented Dooley and Thompson's sexist notions about her.
Jarvis telling Peggy why she can't claim credit for finding Stark's stolen weapons. It's clear how desperate Peggy is for respect.
The reaction to Ray Kzerminski's death. Made worse by the implication that most SSR agents are veterans. Sousa in particular is struck by how similar it was to war time.
Thompson threatening to get Jarvis and his wife deported. Jarvis' face is heartbreaking. Especially when you learn later that his wife isn't a British citizen which would mean that if she and Jarvis are deported they would become separated in different countries in a time when communications past borders was unreliable and without a financial sponsor chances of ever reuniting would be slim to impossible.
There's also some fridge horror attached to this threat if one knows their history; sending a Jewish woman back to Hungary just before the Communist party took power would be bad for her health, to say the least. Jews were considered a specific nationality under the law in the Soviet states, and were denied rights (or imprisoned, or put it internment camps, or killed) based on their being Jewish.
Kzerminski picks up that Sousa has feelings for Carter. His advice? Give up. Because there's no way that Carter could love a cripple after being with a specimen like Captain America. Sousa's reaction is just heartbreaking. Doubly so when the audience has known all along that Peggy fell in love with Steve before he got the super-serum.
The Blitzkrieg Button
Sousa talking about how the only reason people show him any respect for his service during the war is because they feel pity for him getting crippled during the war.
Peggy utterly losing her trust in Howard after he uses her to get a vial of Steve's blood. Followed by Jarvis telling him it hurt more than any other time he's had to lie for him.
The whole conversation between Peggy and Howard after she finds out he lied is utterly heartbreaking, but the standout moment is just one line:
Howard Stark: I know how much Steve meant to you because I know how much he means to me!
The statement was probably not meant to be taken as romantic, but if true it doesn't make it any less heartbreaking.
Thompsons condescending speech to Peggy about a womans place in the world, doubly so since he gives it in the midst of her realization that Howard has used her.
Peggy summing up what she's learned after the episode's events: "I can trust the actions of the men who don't respect me more than the ones of those who do".
The Iron Ceiling
Peggy tearing up Jarvis' card, and latter rebuffing his attempts at reconciliation.
The flashback to Dottie's childhood. She's held in a school full of likely kidnapped girls, who are indoctrinated and trained into Child Soldiers. There's a small moment of love when Dottie steals a loaf of bread and then shares half with the girl bunking next to her... only for the next time we see them they are made to fight to the death. Dottie is forced by her teacher to murder what's likely her only friend, while she was only nine. No wonder she's so screwed up.
She even shackles herself to the bed like they used to do to all the children there.
Fridge Tear Jerker: It can be assumed that Red Room discourages their students from forming real friendship so they can be effective assassins and living weapons without any sense of sympathy. Dottie's teacher possibly knew that Dottie befriended that girl, which is why the teacher instructed Dottie to kill her to end their friendship.
Ivchenko tearfully apologizing to his cellmate Nikolai after shooting him.
Thompson telling the story of how he got his Navy Cross. He saved his CO and squad from a crew of invading Japanese soldiers, shooting them in the back before they ever knew he was there, but he sounds genuinely haunted by taking life, in spite of his apparent relish for beating up suspects. After he freezes in combat and Peggy has to usher him out, he tells her the rest of the story: After killing those Japanese soldiers, he noticed too late that they were carrying a white flag, the universal symbol of surrender. He then buried the flag before anyone else saw it, and was lauded as a hero.
"I've been trying to tell the end of that story since I got back from the war."
When Dugan and Carter are in the truck:
Dugan: (after Carter throws away his cigar) Hey! Carter: You smell bad enough. Dugan: And you used to be fun. Carter: Yeah, once upon a time. (sighs) Dugan: Yeah, I know. I miss him, too.
A Sin To Err
Sousa agrees with Peggy that he can't shoot her, but still begs her not to run and confirm she's the ally of Stark's the rest of SSR has been chasing.
Sousa: Peggy, don't run. If you run, I'll know it's true. Peggy: I'm sorry, Daniel. (runs away)
The way Peggy says "Steve's blood" when she tells Jarvis why she's going back to the Griffith Hotel, even though she's now on the run from the SSR.
As well as Jarvis' reaction when she says she's going back.
Peggy and Angie's farewell. They don't have time for explanations and it's clear they both think they are not going to see each other again for a long time.
The saddened look on Angie's face when Peggy is arrested and taken in to SSR's car, since she helped Peggy avoiding them before.
Chief Dooley's Heroic Sacrifice. Trapped in a malfunctioning vest of Howard Stark's that's going to explode at any moment, he tells the SSR staff to tell his wife, "I'm sorry I missed dinner." and asks Peggy to avenge him. Then he throws himself out the window before the vest explodes, saving all his agents.
Dooley: Promise me you'll get the son-of-a-bitch who did this. Say it! Peggy: ... we'll catch him. Dooley: Atta girl.
Peggy's answer to a question of why she didn't come to the SSR about Stark being innocent.
Peggy:I conducted my own investigation because no one listens to me. I got away with it because no one looks at me. Unless I have your reports, your coffee, or your lunch I am invisible.
The look on Peggy's face after Dooley fires her from the SSR.
This scene is not only a Moment of Awesome for Peggy telling off Dooley, Thompson, and Sousa for how each of them view her, but also a rather a sad Call-Back to a previous episode of Jarvis telling Peggy that they won't respect her. In this moment, Peggy finally reveals that despite what she said to Jarvis, it actually hurts her on how the people she works with actually think of her.
Peggy's reason for keeping Steve's blood to herself, which she summarizes as, "I suppose I wanted a second chance at keeping him safe." This implies that she feels very strongly that Steve's death was her fault. This post sums up the tear-jerker-iness of this moment very nicely.
Peggy correcting Dooley when he calls her "Agent Carter" by saying that she should be called "Miss Carter" since she doesn't work for the SSR anymore.
He might be a supervillain, but hearing Fennhoff describe what happened to his brother when the Midnight Oil was deployed at Finnow.
Howard's sheer desperation to right his wrong and (delusionally) save Steve is heartbreaking. Peggy even appears to Howard in "the Arctic", holding the shield, and telling Howard she's proud of him.
He also calls Cap the one good thing that's come of one of his creations, while we know he won't live to see how much good his son will do.
Howard: Peg, all I've done my whole life is create destruction. Project Rebirth was— He was the one thing I've done that brought good into this world.
Peggy once again stuck on the other end of a radio while someone she loves is about to die tragically in an airplane. In Captain America: The First Avenger, it was Steve crashing into the ice. In this episode, it's Howard Stark, under Fennhoff's hypnosis believing that he's found Cap and he's going to "save everyone", in reality about to nuke Manhattan with the Midnight Oil gas. Peggy breaks down in tears trying to convince Howard that what he's doing isn't real.
Peggy:Howard, I know you loved him. I loved him, too. But this won't bring him back. Howard, you are the one person on this earth who believes in me. I cannot lose you. Steve is gone. We have to move on, all of us. As impossible as that may sound, we have to let him go.
Jarvis realizing he is the only one with experience in flying a plane, and thus the only one who can shoot Howard down, whom he clearly loves. His expression and tone of voice the whole time he's preparing to shoot Howard break your heart - he hates what he's about to do.
Dottie's speech during her fight with Peggy hits a nerve too. Her voice even cracks at one point.
Dottie: I used to be so jealous of girls like you. I would've done anything to walk like you, to talk like you... But now, I can be anybody I want.
Thompson taking the credit was a dick move, but look closely at his expression: he knows it's wrong but he can't help himself. Despite being somewhat a better person at the end of the season, and despite some new respect for Carter. Thompson is still trapped by his past lie and self image and goes out of his way to enforce that image. Even when deep down he knows it's wrong and self serving. He's trapped by what is expected of him and of his own need for validation.
A View In The Dark
Sousa absolutely losing it in his office when he thinks Peggy has been killed, and his relief upon seeing her again.
Peggy losing her composure after seeing Wilkes might not have made it out.
Wilkes' exasperated resignation when a racist assumes Peggy is in danger because she's standing next to a black man. He even tries to calm Peggy's anger about the situation, being so used to it he can't be bothered to stay angry about it for long.
There's also the fact that, if you know anything about the era, Wilkes has to be completely aware of what could happen to a black man caught in the company of a white woman, especially if he was aggressive to the owner. The survival strategy of keeping your head down to avoid getting killed was and still is common for many people of marginalized and victimized groups. And that's probably been his entire life.
Smoke and Mirrors
Peggy and Whitney's past. Both girls had big dreams of becoming something better (Peggy as an Action Girl, Whitney as a scientist) but were squashed by their mothers who didn't believe such dreams were appropriate for women.
At least Peggy had her brother, and her home life didn't seem anything other than average. Whitney grew up with an unpleasant, neglectful mother who placed her sleazy boyfriend's needs before her own daughter's, and blamed Whitney if he was ever unhappy. And as Whitney grew older, her mother began to show resentment and envy towards her that she could actually make something of herself. She looks gleeful when she throws the University of Oklahoma's rejection letter to Whitney's face, asking her if she truly thought a girl would ever be accepted into a school like that.
Peggy's brother's death. Unlike their mother, he encouraged his sister to become a spy despite Peggy having given up on her dream. It is only when he is killed in the war that she finally continues it.
Peggy's reaction to Michael's death is absolutely heartbreaking. She is watching from the window as her mother talks to the soldiers and immediately understands when she sees her mother breaking down. Then she starts sobbing while saying her brothers name in a manner that you've never seen Peggy before.
The Atomic Job
Violet's realization that Sousa (who'd proposed earlier in the episode) didn't tell her the truth of why he left New York, telling him to his face that he's in love with Peggy. He can't even deny it.
Jason vanishing right in front of Peggy again.
Life of the Party
Poor Ana getting hit by the harsh reality of the dangerous missions her husband and friend Peggy are on every day. Jarvis' Adorkable nonchalance to it only adds to her horror.
If you watch Ana near the end of the scene when Peggy gets off of the opposite side of the bed, instead of trying to aid her friend she retreats from the bed into the corner of the room.
Whitney's husband calling the Council together to expose her and have her killed. It's clear he didn't come to the decision lightly, and there are tears of guilt in his eyes as she's strangled...which quickly turn to tears of horror when she kills half the Council and then turns on him.
As much as she deserved it, it's hard to watch Dottie break in minutes after being tortured by Whitney. You can see her crying out of sheer terror.
Whitney casually shooting Ana in the stomach to slow Peggy down after she kidnaps Jason Wilkes. Jarvis is all but numb with grief at the prospect of losing her.
When Peggy calls Sousa to update him on the situation - and to reach for a friend - she's instead greeted by Vernon Masters, who has installed himself as the new chief of SSR Los Angeles. The episode ends with Peggy and Jarvis sitting in the hospital waiting room, all their allies hurt (Ana and Sousa, not to mention Peggy herself), powerless (Wilkes) and gone (Dottie).
Dottie telling Peggy that she cannot comprehend how deep 'the rot' in the SSR goes becomes this, as a reminder that for all the sacrifice Peggy makes to save the world, it will be for nothing, as the SSR has already been infiltrated by HYDRA.
The Edge of Mystery
A massive case of Mood WhiplashShortly after Ana wakes up in the hospital and appears to be on the road to recovery the joy turns to heartbreaking as the Doctor delivers the news that they saved Ana's life at the cost of her never being able to have children
Prior to this, there is the long monologue from Jarvis where he tells a comatose Ana all the things he will do for her from here on out, up to and including keeping her safe. To hear the voice that for so long has been associated with comic relief to be so utterly broken is devastating. Sure, she wakes up at the end, but neither Jarvis nor the audience could know that.
A Little Song and Dance
Peggy and Jarvis' entire argument on the road. Seeing two close friends get so angry, hurt and lash out at each other is heartbreaking enough, then just as Peggy concludes her talk by terminating their partnership and go their separate ways after they escape the desert Jarvis has to confess that he knows his wife can no longer have children and he hasn't had the guts to tell her.
Jarvis: You rescued Dottie Underwood to assuage your conscience, and Ana - my wife - paid the price!
Peggy: Leaving Dottie Underwood with Whitney Frost would have been tantamount to murder, and unlike you, I am not a murderer!
Also doubles as Harsher in Hindsight, as Jarvis' and Peggy's argument would foreshadow the events of Captain America: Civil War, where it depicts the fallout of Peggy's first love Steve/Captain America and Jarvis' future surrogate son Tony/Iron Man.
The fate of Whitney Frost. Having all the Zero Matter forcibly sucked out of her shatters her mind, and she ends up in an asylum thinking Calvin is still alive and this time fully helping her to regain her power. Manfredi looks in with a heartbroken expression, and is then told he can't even give her the roses he brought, as she'd use the thorns to hurt herself.
It can be pretty heartbreaking to realize for all the struggles and victories Peggy goes through, for all the things she has seen and done, she ends up a bedridden dying old woman in the late stages of Alzheimer, barely able to remember the one person she wanted to see again for all her life. And even worse, her efforts to save the world are slowly undermined over time.
It's difficult to see Howard Stark in the show for several reasons: