Theories of a Freighter Pilot
I'm no scientist, I'm just a freighter pilot, and while I generally give all this alien business a wide berth, I can't help but to wonder a bit, and I recently found myself poking about these dusty old ruins in search of answers. I may have found a few. We've all heard about these hyperspace interdictions by some strange alien craft. Pilots report they've been pulled out of hyperspace, scanned and left to go on about their business while the strange ships go on their way, disappearing by some unknown means, leaving equally strange wakes behind them. Plenty of folks are crying "Thargoids", but... I suspect this may not be the case.
Having researched the Ruins to the fullest of my abilities, I've learned a good number of things about the race that left these - they're being called The Guardians. We've learned they were similar to humans in many ways - right down to their self-destructive natures. Turns out these Guardians wiped themselves out in a civil war, a war they fought with bioweapons. Consider these excerpts:"[...]As well as biological warfare agents, they also created creatures expressly for use in battle, and these remained effective even into the modern era." and "[...] when it came to large-scale destructive weaponry they relied on bespoke biological weapons."
And combine that with their affinity for Artificial Intelligence, as evidenced: "[...]Although the Guardians had used computers for generations, it wasn't until the development of artificial intelligence that they truly entered an information age." and "[...] It appear the the development of AI increased their technology very quickly. This sudden increase in computational ability – a result of the new implants, allowed the AIs to adapt and eventually evolve true sentience."
And what was the nature of this war? Why nothing more than the oldest story in history: Religious Conflict. Consider: "[...] The tipping point that gave rise to organised religion amongst the Guardians doesn't appear to have been the creation of thinking machines, but other technological developments - in particular a kind of implant that interfaced with the brain. Up to this point, biological enhancement and repair had utilised only organic-based systems, so this sudden change frightened many." as well as "[...] There was an anti-technology movement that rejected not only specific developments, but also inventions such as virtual reality. The loose customs associated with their affinity for nature formed the basis for a new belief system. It evolved rapidly - almost as quickly as the technological advancements produced by the scientists and machine intelligences. It's interesting to note the parallels with human-made sentient technology, and how its development threatened humanity during the golden age of technological advancement. The growth of this new religion divided the population, and conflict soon erupted." and "[...] the Guardians' homeworld served as a powerbase for this new religious order, which eventually succeeded in ostracising or exiling all of its opponents. I can find no other reference to these exiles in the historical record. This development should have resulted in peace, but a further division arose over the fate of the AIs. At that time, the AIs were virtual entities, and so were reliant on the monolith network to exist. Because this made them vulnerable, they searched for a way to achieve independence from the network. Their research aroused the fear of the abolitionists, who used violent methods to prevent the AIs from achieving independence, and even to combat those Guardians who accepted the AIs." and finally: "[...] But during the first civil war, most implanted Guardians were exiled, and the AIs recognised their vulnerability. They responded by developing their own operational hardware, independent of implanted Guardian users. Frustratingly, the details of these mechanisms have been purged from the record, possibly by the religious extremists who formed the last of the Guardians' species."
This leads me to believe that these alien ships that have been encounters are not what has been speculated at all, but rather are relics of a long-forgotten war by a long-dead people. These craft are, in fact, the very biological weapons created by these Guardians, that were ultimately responsible for their extinction. Consider this: "[...] It appears that the Guardians approach to warfare vastly changed as the war continued. Warfare was conducted using automated battle fleets. At first these were controlled by the Guardians via brain implants, but later they became entirely autonomous."
It may be that, when these craft stop another ship and scan it that they are looking for their ancient enemies - the Guardians. Perhaps they'd react different to a craft carrying Guardian relics.
But what do I know, I'm just a freighter pilot after all. I leave the xenoscience to those better suited to it.