Fears of cancellation have overpowered the depth I saw in this episode.
The conversation Finch had with The Machine was touching and revealing. It reminded me of the final words Data had with Lal, the dying daughter he created in “The Offspring” (ST:TNG 3.16), in which she thanked him for her life.
Finch was addressed as “Father,” not “Admin.” The Machine's apology for failure, questioning her/his/its life purpose and thanking Finch for creating it showed how much it has evolved beyond hardware circuits, programming code and a Boolean algebraic perception of the world. The Machine has become, as Mr. Spock might have observed, illogical – not unlike the humans it protects.
A whole lot of gray was stirred up in Greer's assertion that Samaritan is the Good Guy in the AI battle. The current condition of the world makes it hard to deny that Humanity needs an angry, Old Testament-style Yahweh ready, willing and able to smite all who offend it with corrective action. On the other side is the Machine, allowing Humanity to have free will up the point where it must intervene. This offers plenty of philosophical separation for continuing conflict.
If CBS had definite plans to ax POI, it had a perfect opportunity to end it all in the hail of Samaritan bullets Finch, Reese and Root faced (and would probably not have survived in reality) as the episode ended. The door was left open to what could be an incredible fourth season.
I'll hang on to the hope that this was not a series finale.