Nick Fury comes with a squad of Spider Slayers to take Peter, and the Fantastic Four arrive to help Peter.
Mr Fantastic: Why don't you tell us what is going on here? Peter Parker has done nothing wrong. Nick Fury: Well, I'm kind of in the middle of a domestic military operation, Richards. So follow my direct order and go home!! Human Torch: Yeah, well, I have like three friends in the world. You aren't doing this to one of them.
One of the most shocking and heartwarming moments comes from Ultimate Marvel Universe's Scrooge, J. Jonah Jameson. In the midst of Ultimatum, with New York destroyed by a tidal wave and countless thousands dead, Jameson and the Daily Bugle staff are holed up in a shelter in New Jersey. As everyone else is calling loved ones or despairing, Robbie approaches Jameson, who launches into a broken, melancholy speech about how he was completely wrong and Robbie had always been right. In the midst of the devastation, Jameson looked out of his office window to see Spider-Man dive into the flood to save a drowning woman, and the journalist was overcome with shame and self-loathing. Jameson, who is characterized by hubris, admits to his faults and proclaims Spider-Man a true hero. A Tear Jerker at the same time, seeing the man so broken and pitiful.
Later, in the Death of Spider-Man: Prelude arc, Jameson, who has learned Peter is Spider-man, confronts Peter in his office. Peter is sick with worry because he knows Jameson knows, and hadn't spoken with Jameson until now, hoping the problem would go away. But then:
Jameson: I think you realize that if I was going to out you, I would have by now. I'm not. I'm not going to out you. Peter: I was hoping... Jameson: I thought about it. Oh, I thought about it. And it would sell me more papers and bring more business to this website than any other story on planet Earth... But it seems, after a little soul searching, that I discovered I would cut off my own hand before I would do that to you.
After Peter takes a bullet for Captain America (Who gave Peter a "The Reason You Suck" Speech over his lack of maturity the last time they spoke), Peter remarks that Cap must think he's a complete idiot for doing that. Cap responds by pointing out that Peter just took a bullet to protect someone else, and tells him that "when you grow up, you'll be the best out of all of us."
Issue #2 shows us that Thor, while sad that Peter isn't among the living, smiles because he knows that Peter's soul has ended up where he deserves to be... The Heroes Banquet of Valhalla, the Ultimate Marvel version of Heaven for fallen heroes. What makes it extra heartwarming is that he's not the only hero there.◊ Doubles as a Tear Jerker if you take it as Thor simply imagining things.
After Spider-Woman takes Miles into S.H.I.E.L.D custody, Nick Fury & Tony Stark both call him out on wearing Peter's costume, as expected considering they both liked him. But who else does this? Hawkeye, whose few interactions with Peter involved Clint being a Jerkass to him.
In Cataclysm, Miles offers himself to go to the 616 Universe and get Reed Richards' help when told how dangerous the mission can be. If you look off in the side, you can see Clint crossing his arms and smiling as if he is proud of the kid for showing the same guts that he knew Peter had. It is a nice touch.
There's also the rather cute image of Nick Fury escorting Miles around the Triskelium, holding Miles' hand the whole time.
616!Peter learning about his Ultimate counterpart's death — after stopping a mugging, the man Peter saved thanks him, but points out "That costume is in terrible taste" and when Peter tells him that he genuinely doesn't understand what he's talking about, he's told "We need all the heroes we can get but that was Peter Parker's. You really shouldn't be wearing it."
After finally seeing the proof of his Ultimate counterpart's death, Peter heads straight to May's house, where he naturally meets her and Gwen Stacy. Although the meeting is naturally painful and confusing to start, it gives May and Gwen a chance to find closure with the death of their own Peter, and see, even if though the proxy of 616 Peter, that he would've grown up all right.
Jessica's confession to Miles about why he needs to be Spider-Man as well as confiding in him the fact that she's a clone and has deeper issues.
Aunt May letting Gwen stay with her and Peter. Also a Tear Jerker.
In Cataclysm: Ultimate Comics Spider-Man #1, at least some of the cops seem to have fully embraced Spider-Man as a hero. When one cop sees Miles for the first time in his costume after his year-long retirement, he excitedly runs up to him and gives him a big hug, before saying that seeing Spider-Man's webs always means the police have a helping hand.
In Cataclysm: Ultimate Comics Spider-man #2, Miles helps a kid find his father by webswinging across the city with the kid in the midst of the chaos. When Miles finds the parent, the parent gleefully thanks Miles for helping his kid and tells them that there is no way that the man could ever repay Miles for returning his son to his child.
Bombshell, who was just told that she could not be a hero or use her powers or else she would be arrested, stopped a robbery from happening. She is so proud of herself. This was her first act as a superhero.
Spider-woman: Nicely done.
Bombshell: That was my—that was the first thing I have ever done as a superhero.
Spider-woman: Is that right?
Bombshell: First time.
Spider-woman: It suits you.
Miles and Jessica start helping with people who survived in a plane crash. Jessica opens a hatch while Miles goes inside the plane to look for survivors. He finds one and it is J. Jonah Jameson. After Miles escorts him out of the plane and into immediate safety, JJJ promises to change Miles' life after this disaster is all over just like he did for Peter.
Ultimate Spider-man 200 is littered with heartwarming moments.
Cataclysm: Ultimate Spider-Man #28 has a scene where Miles runs into some cops, who are absolutely thrilled to see him and shower him with praise, even when he says they used to "pull guns on him". It gets even more heartwarming when you consider that this line is being spoken by a black teenager in the wake of Fergusson.
MJ and Peter finally get their happily ever after.