With the revelation that they are being taken, I immediately thought of Pria, from The Orville. Essentially, she was an agent from the future sent to steal The Orville for future collectors. The unidentified ship is clearly extremely powerful despite its small size, which screams time traveller to me. And they seem to be taking examples of ships from all different empires, as if for a collection.
My other thought is that it's some party trying to turn all these empires against The Federation, as, to date, no Starfleet ships have been attacked. It's not unreasonable that their neighbors could see that as suspicious, and conclude it's an advanced Starfleet attack vessel.
Overall, I thought it was fine. I think it got hit a little harshly by critics. It's not terrible (read: unwatchable), but it's pretty firmly my least favorite Star Trek series.
Without actually looking through the full episode lists, and just going off what I remember of each season, here are my gut ratings:
S1: 3/10
S2: 5/10
S3: 4/10
S4: 8/10
Overall: 5/10
Going a bit more into my thoughts in each...
Season 1 - 3/10
Pros:
Cons:
Season 2 - 5/10
Pros:
Cons:
Season 3 - 4/10
Pros:
Cons:
Season 4 - 8/10
Pros:
Cons:
Conclusion
I think Discovery suffered from one main issue, in multiple way: season-based plots. Since every season had a single main plot, any issues with the plot ruin the whole season. We don't get standalone great episodes like in the old series, which you could watch at random. You kinda need to watch the whole season. Furthermore, since each season had to have a big plot, every season is dealing with a huge issue. It's exhausting being in an existential crisis the entire time. That's the feeling we have in our real world right now. That's the reason I watch Star Trek; it's a glimpse at how the future might be brighter. Discovery never felt like a promising future. It felt like we are going to be struggling for our lives for the next millennium and more.
So, I still enjoyed it as a piece of media, and a part of the Star Trek canon, but it's not a show I see myself watching again and again like the rest of the franchise.