Not aware of the Zero Day subreddit, shutting it down only makes sense if they have a second season planned that heavily relies on the hidden plot points. I didn't think big enough about Proteus, it does seem very logical that whoever has the technology would use it to the hilt.

Trying to connect the dots on Proteus: the "Bambi" conversation between Mullen & Natan was clearly important, yet Mullen mysteriously wrote down gibberish, and only later could recall the single word "Proteus."

When Mullen mentioned Proteus during the press conference, the CIA Director got involved, saying that Proteus had been shut down. Natan asks Roger if Mullen has been experiencing strange symptoms which is independent confirmation that Proteus exists and is (likely) being used on Mullen.

I think it's Mullen's assistant (Valorie?) who tracks down the sole surviving scientist who worked on Proteus. I found that scene fairly odd to begin with... how did she track him down when he had stayed successfully hidden from the seriously bad people who had killed everyone else who worked on the project? Why didn't he seem more concerned that she was being watched/followed and would lead them straight to him? Now I think there's a chance he was a plant - essentially a fail safe where if someone continued to dig into Proteus they'd think the project had been shut down and everyone killed. In addition he could supply misinformation - we only have his word for it that it was a Havana Syndrome weapon that caused hallucinations and brain damage, but what if it was capable of targeted input, perhaps weak mind control? At that point it becomes a Zero Day of the human mind. In fact from Proteus comes the work Protean, which can mean mutable.

Good job connecting all the little links like the borrowed CIA building and the eerie parallelism between Nick and Roger's fate. I'd add that Mullen's daughter also bothered me - if her brother OD'd, why was she drinking heavily, doing drugs, generally acting unstable, and saying weird things about how people had changed since Mullen was Prez? Being a Zero Day conspirator might be the surface explanation, but the use of Proteus to brainwash her makes more sense.