After Kate thinks that Constance implied that the former would give them up if she was captured, Constance said something like, "I was going to say 'If you get captured, don't worry, we'll find a way to save you." This compassion was unexpected from the youngest member and surprised everyone. Kate replied similarly to "Sorry, Connie girl. I forgot you're not a total crab."
After the return of his memories, Milligan laughs heartily which makes everyone jump as they're not used to his laughter. "After all these years of acting like the saddest man alive, Milligan now acted as if he were the happiest man alive - and perhaps he was. Having so long ago exited his life as a father, he had now, at long last, entered it again".
When Milligan and Kate are sitting together at the table in Mr. Benedict's house near the end of the book. Milligan plucks her chin with his hand as she beams, but then realizes he took a marshmallow from her hot chocolate and ate it. She giggles and calls him a thief. After being separated from each other for so long they finally get to have the little moments of the father-daughter relationship.
When Reynie cries when reunited with Miss Perumal as she asks if he'd like to be adopted by her. She asks if she can take that as a yes.
When the 'Shortcut' comes to shore, meaning that Captain Nolan was willingly seriously damaging it because Reynie asked him to.
When Mr. Benedict and Joe Shooter hug near the end of the second book, after Mr. Benedict had been a prisoner.
When S.Q. tells the children that he doesn't hold any ill feelings towards them for tricking and leaving him in the second book and Reynie cleverly finds a way to talk to him indirectly by talking to his friends to tell S.Q. they don't blame him for anything. When S.Q. leaves, Reynie almost called after him, forgetting the consequences in the heat of the moment.
In the third book, Reynie feels pressured as the leader to solve everything. Kate tells him that she nor Sticky nor he can do any of it alone, which is also moving as in the first book Kate believed she didn't needed anyone but herself. Kate realizes that she too, unaware, had often looked to Reynie to solve things and said she guessed that was her own way of putting pressure on him. She said she wasn't going to do that anymore and that she wasn't counting on him to solve their current situation. "I'm counting on 'us'."
When the Society sees Milligan in the prison they all feel so relieved and happy. Kate even runs to him and he picks her up in a hug as he laughs in relief in their safety.
Curtain clinging to S.Q. after S.Q. saved him from the crane. Before the former fell asleep it was noted that there was something in his eyes, and it might had even been hope.
In the original The Mysterious Benedict Society book, Reynie reflects on how sometimes he would tell the memory of some teasing he had endured to Miss Perumal, who would never offer advice, which would have been useless, but would only nod and cluck her tongue, smiling sadly, as if the memory were her memory too, as if they shared it.
Well, he supposed they did share it, now that he'd told her of it. And somehow this had always lightened its effect on him — even, on occasion, cheered him right up.