Spock breaking up with T'pring for Chapel makes me sad. They could have been so good for each other. And I just now realized: Spock never ends up getting married (that we know of).
Maybe I'm just projecting human emotion, but I feel like that explains some of the more morose/melancholy demeanor seen in his later years. Always put the needs of the many first, even to the very exclusion of his own needs.
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.