My own take on it:
I think there were some interesting choices made in the story that are not so much clues to the resolution but instead groundwork.
First there is the title of the episode - “Identity”. It’s a title choice that has many layers. Obviously it’s referring to who Isaac’s people really are, but it can also be referring to Isaac himself. Isaac has formed his own personal identity while on the Orville. As he mentioned in an earlier episode, his subroutines have been altered to the point that he needs the Orville crew to function. Keeping them alive is his own self preservation in a way.
Next we start out the episode with Isaac playing something like 8th dimensional chess. Isaac boasts about how he is smarter than everyone, but he’s also proving his ability to form complex strategies and win every time.
Then Isaac shuts down. As we later find out, this was done remotely by his people from a vast distance away. If it can be done to Isaac, it stands to reason it can be done to any of his kind - potentially to all of them no matter where they are.
Isaac returns home and is rebooted. It is stated he will be taken away to be disassembled and re-integrated; but the only thing that happens is an interface and possibly a download. This is different than the Kaylon receiving Isaac’s reports - this was a direct connection to Isaac himself. After the interface, Isaac is *not* disassembled and is returned to talk to the crew of the Orville. Why did the Kaylon change their mind?
Isaac goes through his good byes and the party, but he is acting a little differently. After receiving the drawing, he leaves. Before leaving the ship, Isaac takes a long look at the drawing and then discards it. Why did he look at it like that? Why didn’t he refuse the drawing when it was first offered?
Lastly, the Kaylon spring their trap; but they don’t kill the Orville crew on the spot? They only kill those who are attacking them. Why keep the crew alive? Why take the ship? The Kaylon don’t need any of them.
I think Isaac is playing a long game; and like his people were doing, Isaac was stalling for time (which made it necessary to act differently to the crew so as not to give himself away to his people). Isaac has infected his people with his subroutines in that download, and they are being altered to have an affinity for the Orville just as Isaac has. Isaac knew this would happen, but it takes time. Ty’s exploration of the planet messed things up a little causing the Kaylon to spring the trap early before their minds could be changed, but it’s still processing in their systems.
The interesting thing is this. What if it doesn’t work? There is another option. Would Isaac push the off button of the Kaylon species? Makes for an interesting discussion on genocide, and it could potentially make Isaac the last Kaylon in existence (making him more like Data). Of course, Isaac won’t be viewed the same by humanity after this; but killing his entire species to save the Union would go a long way toward the Union (and the Orville) giving him a second chance.
And the massive punchline to the whole story? If Isaac pulls all of this off, he’s going to prove he is smarter than everybody else.
Just my thoughts on it. We’ll see where it goes!