- Elena salvaging Drake's ring after Nate leaves it with sir Francis.
- The final scene where we discover that Elena's all right and she and Nate finally share that kiss. Final line in that scene doubles as a Crowning Moment of Funny as well.
- She followed Nate to Tibet. Was there ever any doubt who Nate's gonna end up with?
- In Nate's diary, amongst the mementos, goofy doodles and notes about treasure is an unexpected fuzzy moment - a detailed sketch of Tenzin's tiny daughter, Pema, wearing a sweet little smile. Awww.
- The flashback to Nate's childhood and Sully turning on Marlowe's men to save a kid's life.
- Chloe's reaction when Charlie's hallucinating due to being drugged, and trying to kill Nate. A far cry from how selfish she was in the second game, she constantly tries to help him snap out of it. It's likely that if she wasn't there, Sully would have shot Charlie point blank.
- The fact Sully was willing to shoot Cutter in the head just to save Nate. He even distrusts him for a while afterwards, until he helps him after Cutter breaks his leg.
- At the closing of the second act, Nate staggers back to Elena, utterly exhausted from being held hostage and trying to find Sully. Nate's about to turn around and head back out, but Elena makes him lie down and rest, with his head in her lap, and even strokes his hair. Made even more adorable when Nate takes her hand, and apologises to her.
- Also doubles as a Crowning Moment of Awesome for Nate. Sure, he's been beaten within an inch of his life, he's tired, he's hurt, he damn near drowned, and he clearly can barely even stand up. But Sully is in trouble. That's the only thing that matters to him.
- And a Crowning Moment of Awesome for Elena too; she's all ready to go after Sully herself until Nate shows up at the last minute.
- The fact that losing Sully is clearly what Nate fears the most during Drake's Deception.
- The end of Drake's Deception with Sully's fatherly speech to Nate, and Nate finally wearing his wedding ring again. Made all the cuter when Elena mentions she's sorry that Nate lost Drake's ring, he just responds that he replaced it with something better, and shows her his wedding band. Aww...
- In the Atlantis of the Sands Sully and Nate catch a glimpse of a beautiful solar eclipse, and the way they are in awe of how spectacular a sight it is says so much. For the first time in a long time they are able to enjoy the beauty of nature and the wonder of adventure, a quiet moment with no complications and only joy. Also the pride that is evident in Sully's tone and expression is heart warming, this is a moment between him and Nate where they can stand as equal adventurers, almost like he's looking pridefully at his own son at the height of his career. It's fortunate that the scene of Sully being struck down in such a powerful emotional moment is just a hallucination. In light of that it's also heartwarming to think that Drake's hallucination, his inner desires, reflect his desire to have such a touching moment with Sully.
- A somewhat dark example, but at the end of the game when Marlowe is trapped in a pit of quicksand, Talbot desperately attempts to reach her himself and then immediately forgets all of his animosity towards Drake and begs him to Save the Villain, proving that for all his evilness, he really does care about Marlowe.
- In Drake's journal, nestled between sketches and notes about artifacts is a detailed sketch of Elena. Awww.
- Nate helping Chase find the Golden Abyss despite being worried about Dante and Guerro's men chasing them, he's doing it because he knows he much the discovery means to her. Sully even questions him about this after Chase gets captured and he wants to mount a rescue and the way he talks about her passion is a rather unique side of Nate not really seen before.
- When Nate pushes Chase into a fast-moving stream to save her from Guerro before joining her at the mouth, she gets really pissed at him for letting Guerro get away with her grandfather's treasured amulet. However he shows that he managed to hang onto it, which gets him a big hug. While hardly an original sort of scene, there's something particularly special about a guy like Nate going to such lengths to protect this girl's amulet, whom he barely knows (and, at the time, is even expressing frustration over her lack of forthcoming).
A Thief's End:
- Nate reuniting with his long lost brother, Sam, towards the beginning of the game. They spend hours catching up, with Nate inviting Sam to have dinner with him and meet Elena.
- When presented with the opportunity to restart their search for the lost treasure of Henry Avery, Nate wants to Opt Out, saying he's done playing treasure hunter. In exchange he tries to offer up someone from his contacts list that he knows could handle the job. Sam immediately turns it down, saying no one has your back better than your Bash Brother and Nate winds up agreeing. It's a poignant moment that emphasizes how strong Sam and Nate's bond is.
- Most of the interactions in Nate's house — looking through a photo album showing Nate and Elena's wedding on the beach (featuring a proud Sully tearing up); Nate warmly muttering "Miss you, pal" as he looks at a picture of himself with Tenzin at Nepal; trying to beat the high score on the "TV game thing"... which is a short section of the original Crash Bandicoot (1996) on Elena's PS1.
- The reason why Sam lied to Nate; he just want to share another adventure he saw that they inherited from their mother together.
- Most poignantly, when all is said and done, for all of Sam's flaws, and the hell he's inadvertently put his brother through, Nate realizes Sam is too good a man to leave behind and fights off Rafe and figures out a solution (sink Avery's ship with a cannon) that allows him to rescue Sam who is trapped under a plank of wood to get free.
- The Reveal in the epilogue where you find out that Nate and Elena have a daughter, Cassie, who is named after Nate's mother. After she discovers their mementos of their previous exploits from the last three games, her parents decide that it's finally time to tell her everything. Plus, Cassie seems to have inherited both her parents' sharp wit.
- When Elena and Nate stumble upon the gathering of the poisoned Founders, sans Avery and Tew, Nate starts going off into an excited ramble about their findings, and Elena looks on. The scene is set up as a near mirror to the beginning, when Nate blanks off into space while Elena talks about her own work, only Elena is staring at Nate. There's sadness in her eyes, but also a glint of familiarity and love. And there is a small smile on her lips that only grows more sure until Nate catches her staring. For all that he's done, and for every right Elena has to never forgive Nate, she still loves him—and that this excited rambling was one of the reasons why she fell for him. And this time, Nate pays attention: he apologizes to her for everything.
- The fact that, for all his flaws, Sam does genuinely love Nate a lot. He's always checking to see if he's alright, helping him when he's in trouble in a fight or catching him when he falls, and he's been shown to be willing to take a bullet for him twice.
- Blink and you'll miss it, but when Rafe threatens to shoot Sam on the cliff, despite the fact that Nate has just found out Sam has lied about whole thing, Nate tries to calm Rafe down and edges closer to Sam with every step, almost as if he's trying to get between Rafe and his brother.
- After Nate is found by Elena, he asks her why she came and she responds she had seriously considered not bothering this time and that her husband's recklessness/lying had gone too far. But in the end, she did because there's still a bond there. Afterwards Nate monologues that he married a girl as talented as himself and almost squandered it over some petty treasure.
- The last scene in the epilogue: Elena puts the photo of her, Nate, and Sully that Cassie found standing beside the treasure they found at the end of the first game. In the book besides the Photo of young Nate and Sam, right above the word SIG PARVIS MAGNA.(Greatness from small beginnings) Reminding us of both Nates in universe humble start, and our first unforgettable adventure with him and the team.
- A very small example, but when the old lady finds a younger Sam and Nate going through her stuff, she points a gun at them. When the old lady points the gun at Nate, Sam's big brother instincts kick in and he steps in front of Nate, telling her to keep her gun pointed at him and not his brother. His care carries on even in adulthood, when he takes a bullet for Nathan when Rafe attempts to kill his brother. It really shows that even with all of Sam's flaws, he truly does care for Nathan.
- In the epilogue Cassie can find a picture of Elena and Sully enjoying a beer on the beach. It's nice to see that after so long, Nate kept his promise of keeping in touch with his old friend and father figure.