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Both branches of the initial route split start with small ones. Walter is obviously relieved to have you join him and Jonathan cries if you choose to side with him. Having people at K's tavern comment on how good it is to see you and your partner getting along makes this better or worse depending on where you end up on the alignment chart and your feelings about the alignment heroes.
Even though the place is full of horrificrevelations, one of the gas-masked workers who works with the kids in the Reverse Hills Building legitimately loves working with them, which is oddly heartwarming.
The entire Neutral route can feel like one. First, Steven congratulates the player for rejecting the temptations of the other routes, then upon your return to Tokyo Isabeau is so relieved to have you back safe and sound that she has to fight to not burst into tears. Later, you're tasked with bringing "hope" to Tokyo, which you do by completing challenge quests. As you complete specific requests and your overall ranking with the Hunter's Association goes up, NPC dialogue changes to reflect the growing hope your actions are bringing to Tokyo. When you finally take the top rank you embark on a victory lap across Tokyo since you've become so famous and beloved by the populace that very presence inspires hope in the people. It's incredibly satisfying, and a great way to get pumped to kick the crap out of the angels and demons threatening the city.
Also after you defeat Merkabah and Lucifer when you return to the bar, you see Hope standing outside, clearly proud of your accomplishments. Inside you find Isabeau, Fujiwara, Skins, K, and Hugo relaxing while talking about plans for the future. Burroughs even notes that the atmosphere seems to have changed to something that wasn't seen in either Mikado or Tokyo yet. And at the end right before the credits roll, Flynn encounters the girl again who transforms into the Goddess and gives him a simple yet nice 'thanks' when the screen cuts to black.
Reading manga with Isabeau in the neutral path. There's no real reason for the scene to be there, but it's happy enough.
It's twisted, but there's something kind of touching about the Chaos ending. Lucifer mentioned earlier that through him, Walter is with them. He wasn't kidding: there was no way he would know about the scene with Flynn, Walter and Johnathan on the top of the castle unless he held onto Walter's memories. Douche he may be, but he's a man of his word. And then in an incredible show of respect, he steps back and declares Flynn to be the superior choice for the King of the new world.
Akira's resolve in both alternate Tokyos. Blasted Tokyo Akira is prepared to take on hordes of demons if it means helping pave the path to rebuilding a Tokyo ruined by Law. Infernal Tokyo Akira becomes the King of Tokyo...because he wants to end the Might Makes Right rule of Tokyo and bring both the strong and the weak to equality.
Curiously, there's another such event in the case you tell Infernal Tokyo Akira you have your doubts about his plan. For a moment, he falters, wondering whether his philosophy is even right, and then Jonathan tells him he considers his choice the best one, and that he knows that it's precisely the hope of ending the violence in Tokyo and bringing true equality that truly makes him a worthy king. Akira is briefly left sputtering at this show of absolute faith in him.