The ending of the Spine boss battle. Red goes inside the Spine's body and literally breaks its heart. As in, slices it in half.
It turns out that The Transistor is the missing control mechanism of the Process, that is responsible for everything people asked for in Cloudbank; buildings, walkways, districts and so on... You get to witness this power by having it build an entire bridge to Fairview seemingly out of nowhere.
The final battle. The entire game enemies have been completely at your mercy during Turn(), overwhelming you when its recharging. While Royce is just as helpless versus your Turn(), you are completely helpless against his. You get a taste of what your enemies have been going through the entire game. So what do you do? Overwhelm him through cold, hard tactics. You've honed your skills by fighting off the Process. He hasn't.
Even better if you use Help(). Royce does have a line for this, mocking you because t you can't beat him on your own. He doesn't seem to realize that Red was never alone, even as Sybil's function savages him.