Missile is a Crowning Animal of Heartwarming, bar none. His peppiness and sheer bullheaded loyalty toward Kamila (and Lynne, but he's more protective of little Kamila) borders on squee-worthy. And to see another version of him spend 10 long years waiting for the right moment and right circumstances to save his beloved ladies is just a whole different level.
And why did he do it? "Because that's what doggies do!"
Even though he's become old and gray over the 10 years of waiting for the cycle to repeat, this line is still accompanied by the youthful yap Missile is known for.
And during the final scene of the game in the changed present where everyone's eating together, you'll notice that Kamila is on the floor playing with an INCREDIBLY giddy Missile, who as far as she knows has just met her. (If she just met Lynne, it follows that she hasn't met Missile.) But Missile probably remembers the old timeline, so he's just thrilled to finally be reunited with his little lady after so long.
Yomiel telling Sissel that for all his powers, he lacks the ability to travel back in time. "If I could do that, I would've saved you."
"These long, lonely ten years... you were my one and only friend. How about it? Do you remember now... old friend?"
The ending. Just seeing all the happy fates you've brought everyone...
"Thanks, Sissel." Then we see the picture Yomiel's been painting of Sissel in the pose we saw earlier.
(Lynne has just told Sissel that she won't put finding his identity above her own goal)
Lynne: But I'm afraid I'm still going to ask you...
Sissel: Ask me what?
Lynne: Ask you to save me. Even though I probably won't be able to help you...
Lynne: I know it's selfish of me. I really apologize. But... I just can't die. Not yet. Not like this. I'm investigating something important tonight. I think maybe that might be the reason. I was killed. But I still want to solve the case, in spite of all that! Am I out of line?
Sissel: ... Didn't I tell you a minute ago that you don't owe me?
Sissel: I'm certainly not gonna treat your life like some kind of bargaining chip. I'll save you. What you do after that is up to you.
Sissel also uses this moment to conclude that he CAN trust Lynne BECAUSE she honestly told him that she wouldn't be able to help him, instead of lying until after she was revived.
After Lynne's first death, the moment where Sissel decides he's "not the kind of guy who can just let a woman sit sneezing in the cold rain." He then possesses a nearby umbrella and floats down to her.
When the Justice Minister finds out Amelie is safe, he smiles for the first time in the whole game. Doesn't sound like much, but it's a surprisingly radical change.
It's also a small thing, but when you first meet his wife, she seems cold and heartless for leaving him and for forbidding his daughter to call him on his birthday - it's easy to assume she left him for selfish reasons. However, it turns out she left him on a matter of principle when he signed Jowd's execution order, and refused to come home unless he reversed his decision - even she thought it was unjust.
Lynne and Sissel's final goodbye, doubling as a Tear Jerker. "I'll never forget you... no matter what happens."
And she keeps her promise right before the credits roll. "We meet again... Sissel!"
The revelation that Cabanela isn't out to get promotions for vanity's sake. He's doing it because he fully intends to help Jowd, willing to accept any scorn from Lynne or others so long as he can make sure his friend doesn't get a punishment he doesn't deserve.