The 39 Clues is about a torn family that must eventually reunite and take on new threats against the world, so naturally every book has at least one heartwarming moment!
WARNING: Spoilers are unmarked.
Series 1: The 39 Clues
- In Beyond the Grave Amy and Dan have one really horrible fight over Grace and her memory. Amy begins to think that Grace didn't really care about them and was just using them all those years. Later on, Amy and Dan remember a time they went to a history museum in New York with their grandmother and they all ate pretzels on the stairs. Grace tells them that the museum was nice but this is the best part. The Fridge Brilliance of that is, when Grace says she likes spending time with them more than the museum, she also means her travels and adventures all over the world too (which they didn't know at the time)
- Dan getting another picture of his parents after he lost the only picture he had of them in Paris.
- Irina Spasky talking about her son's death and how she found her women's polevaulting medal in his pants pocket — he'd carry it around at all times because he loved her so much! And then saving the kids from the fire.
- In book 9, Storm Warning, Amy and Natalie's short conversation, which doubles as a Tear Jerker. Explanation:
- Jonah's dad in the last book when Isabel kidnaps him along with everyone else's families and ties him up to an explosive. Jonah, who never really knew if his father loved him, sees him singing their childhood lullaby on the screen.
- Whenever Amy or Dan run into a relative of their parents, Shep, or Fiske, Amy will see her dad and brother's facial expressions in Dan. Their uncle Shep reminded them so much of their father.
- The last book has many of these, but Grace's last messages top this. Especially at the end, when we see the secret end message and it's Grace (the audiobook makes it really heartwarming where you hear her talking) giving them The Flying Lemur and her base in Madagascar.
Series 2: Cahills vs. Vespers
- In the second series, Evan and Amy's interactions are this a good deal of the time.
- And, as usual, any time when Dan and Amy show how much they care about each other (even if they do think of the other as a "dweeb" and a "nerd," respectively).
Series 4: Doublecross
- Cara and Ian finally kiss in Mission Hurricane. Even better is the context: Ian is extremely happy to give up his leadership position to Amy, and when he tells Cara the news, she immediately solidifies their relationship. She didn't love him for his power, but rather for his Jerk with a Heart of Gold character.