Missile is a Crowning Animal of Heartwarming, bar none. His peppiness and sheer bullheaded loyalty toward 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 master is just a whole different level.
And why did he do it? "Because that's what doggies do!"
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.
Finding out Lynne's detective's badge is actually a toy Detective Jowd gave her ten years ago for being brave, which she's been wearing ever since. D'aaw.
(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... Sissel: ... 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? Lynne: Huh? 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.
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.