- Tony's reaction to Pepper's (apparent) death. He begins to tear up and then suddenly just seems to stop feeling anything, with a look of complete desolation on his face.
- And it gets worse when you think about how this is what Tony has been afraid of the entire film. From yelling at Pepper that he couldn't protect her outside the mansion, to building forty-two suits that are calibrated to protect her as well as him he's tried everything to keep her safe and still failed. Thank goodness it was a Disney Death.
- Tony's reaction to seeing the hologram of Pepper being tortured with the Extremis virus. Never has Tony seemed so helpless. He's nearly crying, and has to look away.
- And then it gets worse when you read Pepper's lips on the hologram while she's being tortured. "Tony, make it stop!"
- Seeing Tony suffering from PTSD is just heart-wrenching overall. The insufferably confident Jerk with a Heart of Gold is breaking down and it's just...it's painful to watch.
- JARVIS shutting down (for the first time in four movies) after the attack on the Malibu house and the flight to Tennessee drains all his power:
JARVIS: [voice slowing down] I think I need to sleep for a while, sir...
Tony: JARVIS, don't leave me now, buddy.
- What kills is how JARVIS' tone was high-pitched and cracked, clearly very distressed from the ordeal.
- Dummy and its junior trying to hold each others' hand as the Malibu house falls apart.
- What makes this especially hard is that they are shown to have an innocent, almost childlike, artificial intelligence, to see them suffering is in such a brutal manner heartbreaking.
- Yinsen's brief appearance, considering what his eventual fate will be.
[after Stark abruptly walks away from his introduction]
Yinsen: Another time, I suppose...
- The flashback in the beginning where we first meet Maya and Aldrich. They both seem so hopeful. Maya dreams of creating a universal cure for humanity, Aldirch is an adoring fan of Tony's who wants to create a think tank to take science to new levels. Cut to over a decade later Maya has compromised her ethics in her obsession to perfecting Extremis and seems broken. Aldrich is driven to acquire power and strength and is willing to do anything and everything to erase the sad little man waiting on top of a rooftop on New Years Eve.
- Killian becomes a Woobie, Destroyer of Worlds when you remember he was nearly Driven to Suicide after Tony stood him up. His life must have been so bad up until that point, it's a miracle that his peering over the edge became a life-changing revelation, even if it was for all the wrong reasons.
- Killian shooting Maya right in front of Tony, just when she'd decided to pull a High Heel-Face Turn.
- The brief shot of Pepper standing at the cliff edge after Tony's Disney Death. Sure, we know he's fine, but she doesn't, and it hurts to see smart, capable Pepper in that kind of state.
- The moment of sheer disbelief as she registers the scene before her, before she can even shout Tony's name.
- The way she screams his name is gut-wrenching.
- When Tony unconsciously calls the Mark XLII and it attacks Pepper in bed, she's so scared, exhausted and frustrated that she goes to sleep downstairs. That combined with Tony's reaction is like being punched in the stomach.
- The bit before that with Tony's visible nightmare. This is no Catapult Nightmare, oh no. This is pain.
- The "bombing" site in Tennessee, loaded with memorials and flowers. When Tony tells that soldier's mother that her son didn't kill himself (and five other people) that day, even if he can't tell her what really happened, it's really hard in a totally banal, real-world way.
- The reason Vice President Rodriguez became a traitor: He was working with Killian so that he could have his daughter's missing leg regenerated via Extremis.
- A fridge one but the bulk of Killian's army are made up of disabled veterans. Some might have been Blood Knights but some — maybe most — likely were once good men and women that fought for their country and then were abandoned when traumatized or disabled. Extremis gave them a second chance but turned them into dangerous addicts with only Killian willing to help them. They were in the hands of aggressive drug dealers.
- Tony signing his fan's drawing: " ERIN HELP ME!!"
- The fact that so many of Tony's PTSD attacks are triggered in the presence of children, period, is a tearjerker. He's obviously having a hard time with everything he's gone through, but all these kids see (with the exception of Harley) is a brave adventure hero with cool robot suits. Adjusting to having a young fanbase (for a foul-mouthed, cheeky playboy like Tony) would be hard enough even without the enormity of what happened in New York. The innocent question about how he escaped the wormhole sets him off, and it must be unbearably hard on Tony to be confronted with the memory of what he's been through that way. It's easy to imagine something similar happening to any other person with PTSD who's now being hailed as a hero, subjected to clueless questions and adulation for their part in something they haven't even fully processed yet.
- While Tony's destroying all his armors he'd summoned to fight Killian and his men was meant to be a Christmas gift to Pepper, and therefore something heartwarming, it's still a little sad.
- Tony's narration at the end, as Maya and Killian are shown how they were at the beginning: full of hope and wanting to help people.
Tony: You start with something pure. Something exciting. Then come the mistakes. The compromises.
- The realisation that, if Tony hadn't been such a jerk back then, the entire plot could have been avoided. Imagine what he, Killian and Maya could have done together if he hadn't left Maya with an incomplete formula, if he'd met Killian on the roof that night. All that potential is gone because of one night that put two people on another, darker, path.
- Maya talking to Pepper in the hotel room, and she tells the story of a man who built rockets for the Nazis. At that point, it's just a sad story, but by the end of the film it's absolutely heart-breaking, because the last three sentences describe Maya so well.
Maya: Fun fact: before he built rockets for the Nazis, the idealistic Werner von Braun dreamed of space travel. He star-gazed. Do you know what he said when the first V2 hit London? 'The rocket performed perfectly, it just landed on the wrong planet.' See we all begin wide-eyed, pure science. And then the ego steps in, the obsession. And you look up, you're a long way from shore.
- It takes a while to register due to how funny the reveal is, but Trevor is a guy who was entirely manipulated by Killian through his addictions, and never had any idea he was participating in real events. And then he ends up going to jail for it, though at least he also has a sizable fanbase. And on a meta level, he's telling this to Robert Downey Jr., a man who knows full well how an addiction can control your life.