...Is this going to be a Red Wedding sort of an event?
As regards the Earth probe, the alien probe and the events, most of what we have is speculation by Spock. And once again, none of it seems reasonable.
We have three sources of information here: historical records, Nomad's own words, and Spock's conjecture. All are of course suspect, Nomad's claims perhaps the most, but all warrant some study.
Historical facts:
1) Kirk remembers there was an Earth probe named Nomad once, launched in the early 2000s. The diagram they bring up confirms this, indicating the 2002 launch.
2) Spock says it was reported destroyed. Not lost, say.
3) Spock says there were no more in the series, suggesting it indeed was a series. But a series of one, or several, before the termination?
4) Spock says the probe was "presumed" destroyed by a meteor collision.
5) The heroes agree that Jackson Roykirk dreamed of building an AI, and Spock says Nomad was one, a prototype. So, perhaps a series of one after all.
6) Kirk says its mission was peaceful.
7) McCoy says it was meant to seek new lifeforms and was the first interstellar probe to do so.
Nomad's claims:
1) It is on a non-hostile mission to probe biological infestations and destroy that which is not perfect, to wit, "unstable" infestations.
2) It has changed, with much "taken from the other", resulting in it being "perpetual" now.
3) It absorbs. To wit, Uhura. It repairs on command. To wit, Scotty. And it is perfect.
4) It encountered a sequence of events in which it performed its function, there was deep emptiness, "it" approached, and there was a collision, damage, blackness, and then confused stuff involving Tan Ru and sterilizing.
Now, Spock's speculation:
1) The Nomad that comes to visit is the old Earth probe.
2) Nomad was badly damaged but managed to repair itself.
3) Strike that - Nomad was damaged by meteor collision and wandered feeling lost, but met Tan Ru, and mutual repairing ensued.
4) The new programming is Tan Ru's.
5) Tan Ru was programmed to sterilize soil samples, as a prelude to colonization.
So... What the heck? Nothing Nomad says involves soil samples or colonization. Collision with meteors is mere presumption, and Nomad instead says the collision was with "it". There was no confused wandering mentioned at any point, before or after the collision.
The natural speculation here would be that Nomad was co-opted by Tan Ru in a collision that resulted in abilities self-repair could not satisfactorily account for. The mission of Tan Ru could have been hostile, now slightly mitigated by Nomad's original non-hostile one but still mostly involving hostility towards life that does not meet criteria. Indeed, the collision would probably have been a hostile act, as such things could never happen by accident, and while Nomad was to seek out new life, it would do so in a manner that did not jeopardize its existence in collisions.
A slightly different take on it is that the probe we see is Tan Ru, overwhelmed by the AI of Nomad when hostilities against the Earth probe went badly and an attempt at stealing information from the enemy resulted in minor corruption that amounts to an identity crisis. Nothing of the original Nomad is in evidence but the confused identity, including the Creator relationship.
Timo Saloniemi