- The end of Raphael #1, where Raphael explains to Casey that until they know who's targeting the turtles, he has to stick close to his brothers. When a disconsolate Casey tries to put on a brave face and say goodbye, Raph will have none of it: Casey is one of his brothers.
- The Donatello one-shot has Donatello musing about how he has a hard time socializing with his brothers, since their interests and personaities vary so greatly. However, Leo is shown listening to and attempting to understand an MMORPG that Donnie likes to play, and is seen at the end of the issue saying that he has trouble understanding the manual. Donnie even muses that "Leo tries to be interested" even if he can't get into it, and that he at least really appreciates the effort.
- In issue #14, when Splinter calls a family meeting of the Hamato Clan, Casey and April think it's best if they leave. Splinter reminds them that it's a family meeting and asks them to please stay.◊ No doubt about it, Splinter and the Turtles see April and Casey as part of their family.
- Every time Tang Shen's spirit comes to comfort Leonardo in his dreams.
- Issue #50 brings us a few:
- When Koya gets the feathers on her wings slashed by Leonardo, Bludgeon immediately rushes to her aid. This, despite being blinded from Donatello/Metalhead's flashbang.
- Bebop and Rocksteady yell at each other when they fall victim to Raph and Mikey's Deadly Dodging, but quickly apologize for the bickering and focus on the Turtles. Dumb Muscle they may be, but it's also clear that they're Vitriolic Best Buds.
- Donatello making a triumphant return in his real body to deal the knockout blow on Bebop and Rocksteady, much to the joy of his friends and family. Complete with a bear hug from Raphael.
- Splinter and Shredder making some measure of peace after the former delivers a mortal wound to the latter. Shredder's last words to Splinter as he commits seppuku come off less as a form of See You in Hell; and more like an acknowledgement between two respected adversaries.
Shredder: I will see you in the forest again...brother.Splinter: I do not doubt it...my brother.
- Shredder, shortly before committing seppuku, tells his granddaughter Karai that all of his harshness towards her was meant to hone her into a worthy successor, and that he truly considers her his finest student. Yes. That Shredder.
- He also vows to Kitsune that though he may die here, one way or another, his spirit will find its way back to her—which she acknowledges by calling him her "Dragon Warrior."
- Splinter, after helping Shredder with his ritual suicide, takes a moment to mourn. Even after all the pain and misery that Shredder inflicted on him and his family—over two lifetimes—Splinter still saw him as his oldest, closest friend.
- Karai honors the outcome of the duel, vowing to return to Japan so she can better train herself to be a worthy leader for the Foot Clan. And she offers Splinter the Shredder's position as leader in the meantime!
Karai: The Foot Clan is my family—my life—and I want only what is best for it.
- While Mikey is understandably shocked and upset by Splinter's decision to lead the Foot Clan, Splinter is understanding of his son's ensuing decision to leave, acknowledging that he needs time to come to terms with what's happened.
- At the end of the issue, Alopex can be seen supporting a wounded Raphael.
- Ever since she was included into the mix, it's been ambiguous just how much Kitsune cared for Shredder, as she's been Playing Both Sides by encouraging Alopex to side with the Turtles and subtly influencing Shredder's decisions. However, when Splinter calls her out on this, she's visibly disturbed at the implication that she never truly cared about her "Dragon Warrior."
And then, come issue 60, when she absconds with what she thinks are Shredder's remains, she privately refers to him as "her beloved."
- In issue 66, Nobody questions Raphael on the nature of his bond with Alopex. Raph expresses his concerns about how such a relationship would work, seeing as he's a turtle and she's a fox, but goes on to admit that he still really likes her. Why? Because the two of them aren't so different, being loners who had trouble connecting with others until recently.
Raphael: ...But you know what? When I'm with Alopex, I don't feel that loneliness at all. That's what I dig about her. And I think...I think that's what she digs about me, too. And we don't even gotta talk about it to know it's true.Nobody: Sounds to me like that "different species" thing ain't as big a problem as you're makin' it out to be.
- Cue the epilogue of issue 66, where Alopex's first reaction to seeing Raphael is to give him a joyful hug.
- In issue 67. Leonardo expresses his frustrations over the conflict of interests he and his brothers have on deciding on what their next move should be regarding recent events. Splinter - who has, by this point, been taking more ruthless actions as the new leader of the Foot Clan - proves that his old, noble self isn't gone by expressing relief that his sons are still capable of being teenagers after all they've been through, and giving Leonardo some fatherly advice for how to lead Clan Hamato in his absence.
- In issue 4 of the crossover with Batman, Raphael accuses Batman of being some sort of thrill-seeking rich boy who has no intention on getting Splinter or the other turtles home and bails. Batman picks him up in the Batmobile and takes him to Crime Alley and the spot where Thomas and Martha Wayne died. He explains that he never wants to see anyone's family shattered by something senseless and asks Raphael to help him help his family. He doesn't get a "yes", but the intent is very clear.