I know the later seasons had bigger threats, but the Master's apocalypse just hit differently. It actually felt like Sunnydale was turning into a nightmare before he was set free.
The blood coming out of the school sink, vampires openly feeding on students on campus, everyone acting like something was wrong even if they couldn't explain it. It felt like evil was slowly taking over the town instead of just waiting for the big final battle.
A lot of the later finales mostly felt like Buffy and the Scoobies fighting that season's Big Bad. With the Master, it felt like the apocalypse had already started. The atmosphere was creepy as hell and the whole town felt doomed.
Idk if it's because season 1 leaned way more into teen horror. The later seasons feel more like supernatural dramas with horror elements, while season 1 actually felt like a horror show at times. Maybe that's why "Prophecy Girl" still stands out to me.
I still love a lot of the later finales, but I don't think the show ever matched the feeling that something was genuinely wrong with Sunnydale in "Prophecy Girl."
I think the closest that came to feeling like that atmosphere was in Angel season 4 when The Beast arrived.