With Fortnite Chapter 3 Season 3 nearing an end, the storyline is ramping up. Whatever Epic Games has in store for Chapter 3 Season 4 has to come to fruition in the coming days, before the next season's events begin. While there hasn't been an antagonist for this season (like the Imagined Order in recent seasons), there could very well be one in the next season.
This season has been all about the Reality Tree and the Zero Point, but the characters have still played an integral role. The Scientist has been key in uncovering the secrets of the Zero Point.
As the storyline picks up, so will the danger and drama. Unfortunately, this has led to the Scientist's disappearance, very likely due to his role in uncovering the Zero Point's true nature.
Fortnite Chapter 3 Season 3 sees the Scientist disappear after uncovering information about the Zero Point
It looks like Chapter 3 Season 4 is going to be far less peaceful than Chapter 3 Season 3. The majority of this season has been fun and lighthearted, with no enemies trying to get their hands on the Zero Point.
However, Chapter 3 Season 4 will likely be a lot more dramatic, and the final portion of Chapter 3 Season 3 seems to be hinting at a change in tone. The Scientist has been arguably the most important character in the storyline, and he seems to have vanished without a trace.
An audio file that was uncovered by @Egyptian_Leaker on Twitter gives some insight into what may have happened to the Fortnite NPC. The Scientist can be heard speaking to Paradigm, who will probably be a very crucial player in the future:
"Paradigm. If you're listening to this... It means I'm gone. I don't know where they took me and I don't know if I'll be back. I promised we'd never leave you alone again. And I promised freeing the Zero Point would be safe. Everything's my fault. So whatever happens to me, I deserve it. I programmed Amie to take care of you and whoever's left. I hope there are people left. I'm sorry it ended like this. I've always---"
This is the last message that the Scientist may ever leave for anyone. He's been helping players complete challenges throughout the season for the Vibin' questline, but he currently appears to be in dire circumstances.
It's unclear who exactly took him, as he only refers to them as "they" and doesn't provide additional details. It could very well be Geno, who was last seen in the finale event of Fortnite Chapter 3 Season 2.
Geno has been a shadowy figure for a long time, operating in the background. He's also been a bit of a mastermind for the IO. Now that he's finally been revealed, it's highly probable that he will be the main antagonist of the next season.
While it's unlikely that Geno himself took the Scientist, he is very likely behind it all. Fortnite players will have to wait to find out.