about the end

[Thaliur]

Hmm, actually I don't see the problem with that hypothesis even with your explanation.
If the Hive connection really spreads like a viral infection, then the "virus" becomes active only after the infection itself, and then takes some time to actually show symptom (this is usually called "incubation period", as far as I know).
So, when Philip got infected, Clarence was not yet Clarence, had no mind of his own, actually no mind whatsoever, until he grew a bit and could use a sufficient portion of Philip's brain to just be Clarence. After all, you need a certain number of brain cells to perform even basic cerebral functions.
And then, during Clarence' "awakening" (in the sewer cavern I guess) he got detached from the hive in some way, maybe due to the artifacts, maybe because Philip was, incidentially, one of those people who were at least partially immune (I think the existence of such people was mntioned in one of the notes either in Overture or Black Plague) to the Tuurngait infection.
When that happened, Clarence became an individual character (like Hugh, if someone remembers that episode of Star Trek ), but still expected to be connected to the rest of the Tuurngait, and thus complains about being "alone", probably still following hat seems to be the Tuurngait's "primary directive" ("There can not be one! There can only be us all!") at first.


By the way, has anyone else noticed how the Borg became less and less frightening over time since they first appeared? First they were able to literally cut a starship into pieces, take over all the crew, including their knowledge and abilities, as well as any technological equipment, detached drones would still be functional, have acces to lots of the Borg knowledge, and try to reconnect to the collective, and later, when their unfrighteningness peaked in "Voyager", they were entirely dependent on that annoying queen person, and would die as soon as she died.
But that's not the point of this thread...