"Rise of the Turtles pt. 2" After recounting the tale of how he lost his wife and daughter, and Leo agreeing that he lost much (he is no longer human), Splinter says that he had gained much as well- his four sons. (Which he originally bought as pets.)
There is another subtle, easy to miss moment in the first part, that took a third watching from this Troper to notice. After Raph beat Leo in the training session he says "Nice try." At first it seems like Raph is being a jerk, but then the camera pans up to his face and the look on his face is nothing but genuine brotherly affection. Again this lasts all of two seconds but it is a genuinely sweet moment as this version of Raph has trouble expressing himself to his family.
To a lesser (and somewhat funny) extent, there's Raph smacking Donnie with his broken staff. If you have a sibling you'll most likely recognize this as simple rough housing. It's pretty clear Raph isn't actually trying to hurt Donnie, and he once again has a brief affectionate look on his face.
The introduction of Spikes was this due to how adorable it is to see a guy like Raph gushing over his pet.
After Kirby decides to cover the turtles' escape from the Kraang's base, and, as a result, gets left behind (which is something of a moment in and of itself, since April's watching it all happen). Devastated, April hugs Donnie, who goes on to reiterate that they'll get her father back. It's still on the sad side of heartwarming, but says a lot.
Any scene of Mikey bonding with Leatherhead, starting with Mikey feeding him "pizza noodle soup". Then after Leatherhead talks to Mikey about what a dangerous monster he is, Mikey says "Maybe you just think you're a monster because everyone treats you that way." Maybe he really is wise beyond his years.
There's something very sweet that Mikey immediately goes to hug Leo when he thinks he'd been crying. He might not be the brightest, but he's definitely The Heart of his brothers.
Raph's worry when Mikey is knocked out when they're fighting Snakeweed. He doesn't even try to hide his relief when Mikey finally comes to.
Also, Raph shouting Mikey's Catch Phrase "Booyakasha!" as he delivers the final blow to Snakeweed, for the same reason. Doubles as a Moment Of Awesome.
Especially heartwarming when, back in the layer, Raph says that he has no problem risking his own life, but not his brothers.
Karai choosing to help Leonardo escape from Snakeweed instead of letting him die. Especially notable since Shredder had already given her a stern warning that she wasn't to let him live the next time they met.
Leo saving the knife she threw at his head as a memento at the end of the episode.
Donnie's concern for April is palpable while she's being chased by Karai.
The turtles are clearly impressed and happy hearing about April's escape from Karai.
Splinter afterwards says one of the most important lessons about being a Ninja is making it back home.
When April is fighting Karai, she says she lost her mother. Karai pauses the fight and is caught off guard, even repeating "you lost your mother?" in a shocked, sad tone, and when April is escaping, Karai gives her a...genuinely sorry look.
After gearing up for their mission, Raph gives Spike a pat on the head, or rather a tap on the head. Later, he picks up a pigeon and uses it to block one of TCRI's security cameras and once his brothers have snuck past the camera, Raph puts the pigeon down and also pats it on the head.
Raph and Leo have clearly patched up their differences, with Raph rescuing him from falling, and even bemoaning his Disney Death, saying he should have been nicer to him.
April tells Donnie after he helps rescue her, "You're my hero."
And at the very end, we have a Dance Party Ending, as the turtles and April celebrate saving the world.
Splinter tells the turtles that when they first went to the surface, he was worried they wouldn't be ready, but states that if the fate of the world had to rest in anybody's hands, he's glad it's in their hands.
A very bittersweet moment when Splinter discovers his supposedly dead daughter is alive and working with his worst enemy.
The ending where Raph admits that he's happy Leo is home in his own aloof way.
The fact that Don kinda goes to Raph over his April-based problems.
We get to see Leo's Big Brother Instinct again, with him threatening Karai to stay away from his brothers from now on. To add to how impressive Leo is here, he still manages to make an attempt to help Karai too during this threat, telling her that Shredder is lying to her about Splinter and imploring for her to believe him about this.
Karai looking at the picture of her deceased mother, Tang Shen. This is probably the first time, we see a girl like Karai with real happiness, instead of the arrogant, snarky kind she usually displays.
Even more so when you notice that she's not even remotely afraid or unnerved of Leo, even though very few humans in this show don't feel that way about the Turtles at least a little (even April was a bit weirded out when she first met them). Even though the little girl is oblivious to the severity of the situation, and even though Leo tries to play the whole thing as if it were her imagination, it's all very sweet that she's innocent enough to look past Leo's being a mutant, refer to him endearingly as "Mr. Turtle", and want to have a tea party with him of all things.
Raph's intense brotherly instinct that comes out when Slash resorts to beating the crap out of Mikey and Donnie.
Even before Slash starts beating them, when he hears that Donnie is missing, Raph makes it perectly clear what his priorities are.
Raph: My brothers come first, no matter what.
Also, when Raph is about to be defeated by Slash, Donnie and Mikey try to restrain him by jumping on his arms even though they're in no shape to continue fighting.
Splinter tells Raph how to drown his sorrows when a loved one is lost, take comfort in the loved ones you still have.
Splinter: Raphael, do you know what I do when I miss my loved ones from the past?
Splinter: I focus on the friends I am surrounded by in the present.
Raph: Thanks, Master Splinter. Hey, what's a guy got to do to get in your little competition?
Mikey Next game is all yours, dude.
Leo: Sorry about Spike, Raphael.
Raph: You guys aren't tooo bad to hang out with either.
When Spike turns into Slash after getting into the mutagen. Its clear that even after his transformation he still cares about Raph with all his heart and truly does want the best for him. Unfortunately this also doubles as a Tear Jerker later on.
Likewise, even after everything Slash had done, Raph still tries to Save the Villain in the end.
There's just something about the little girl's lack of fear towards Leonardo. It managed to strike a cord in multiple fans hearts despite her and Leo's tea party being part of a gag.
Casey saves Raph from being run over by a subway. Later, Raph returns the favor when a Foot Bot knocks Casey off the subway. The two are actually grateful to each other.
When April vouches for the turtles to Casey, he immediately backs off.
Casey: So, they're not the bad guys?
When one of the Foot Bots scan the lair, Splinter instructs them not to let it escape. Casey immediately runs after it to prevent it from revealing the lair's location to Karai.
Casey's entire motivation: he wants to make the city safe from the monsters and ninjas before someone close to him is hurt. Like his dad, his little sister, or April. (The fact that he already counts April as someone close to him really hammers it home)
Metalhead sacrificing himself to save Donatello, the other guys and other captured mutants from the Kraang by maintaining the portal to their prision until they all escaped.
Leo and Mikey trying to console Donnie about Metalhead's "death".
Leo: You were right Donnie, I should've trusted you.
Mikey: Sorry about Metalhead Donnie.
Even Raph became less of a jerk.
Raph: *referring to the portal* Come on you tin can, move your butt!
Slash/Spike and Raph exchanging a brief look as the mutants are escaping...the bond is still there.
Heck all of the mutants (even Snakeweed and Spider Bytez) had some minor moment. Like Mr. O'Neil staying calm and following Donnie's instructions in order to escape.
Donnie refusing to follow Leo's orders of erasing Metalhead's AI since it's basically killing him.
When Donnie says the training session with Metalhead was successful, Leo points out that Metalhead could've ripped Mikey's face off. Considering Leo himself almost got decapitated by Metalhead, which is worse than what Mikey was going through, it was nice to see someone being selfless towards Mikey for once.
Raph helping Mikey when his arm is stuck in the vending machine.
After Donnie is sucked into the Kraang portal and Leo is dragged in trying to save him, Raph and Mikey briefly exchange glances...then charge in after them.