Unmarked spoilers below, as per the Spoilers Off policy
- The opening cutscene
is just generally full of Awesome Art and Awesome Music, but some standout moments are scenes which seem to take place during Xenon's breakout: Cherry shows remarkable accuracy with her handgun, taking out a bunch of drones, while ConneR does a Diving Kick onto a robotic guard before putting a bullet in the back of its head. - In a cutscene in Cherry's chapter, she and Xenon finally find their suspect for the AEsir-fest incident (Ivy) in the depths of an abandoned factory. Ivy pulls out a gun and shoots Xenon, but Cherry manages to grab her own pulse pistol and take her out before she can injure him more severely.
- In Neko's backstory, Yukiko is being threatened by a Loan Shark agency. Neko sneaks up behind one of the criminals and inflicts a devastating Groin Attack. However, another thug manages to knock her out and kidnap her. Neko then escapes from them and gets Xenon's help. But in the end, it's Neko's father Kouhei who gets the coolest moment, using Xenon's tech as well as his own wit to bluff the thugs into thinking that he's the legendary hacker X, scaring them into submission.
- In the Crystal PuNK chapter, Cherry and Xenon notice drones going haywire near a hospital in Node 03. Cherry uses her gun to keep the drones distracted, while Xenon hacks them and turns them all against each other, destroying all of them. Nora later comments that although there were still civilian casualties in the incident, they would have been much worse if it weren't for their intervention.
- PAFF, Xenon, ConneR, and Neko head into the OS space to stop the Architect attack. PAFF carries a virus made by Xenon, and Xenon and ConneR both summon virtual guns to defend themselves. What about Neko? Why, she arms herself with nothing less that a Humongous Mecha!
- The Meta Twist that the game pulls at the end, revealing that the player has been a participant in the story the entire time! It all comes to a head in the Final Boss, with the player choosing to answer PAFF's call and assist her in taking Vanessa down.
- In the climax of the Alice/Deemo chapter, Simon and Alice team up to play Sairai, the song that Alice has been trying to remember the whole time. The game starts the track at Chaos difficulty against a black background, like the AEsir song in the main story. Already a good ending, but what makes it really awesome? After the first verse, the gameplay starts seamlessly switching between Cytus and Deemo, with the beat line stopping at the bottom of the screen and piano notes falling from the top! This finally triggers the tree's growth, and Alice saves Simon from the crumbling game simulation in the same way that Deemo revives her in the original game.
