Having just finished the game, I agree with this youtube user decyphering of the Octagon messages:
1. Sam must assimilate.
2. Sam, Emma, go to Saturn.
3. Sam must protect Emma.
4. The others must not assimilate.
5. Infinite universes combine.
6. Protect Emma, not other crew.
7. Emma must assimilate.
8. Jim must not assimilate.
9. Sam must kill Jim.
10. Infinite universes combine.
11. Sam, Emma, merge.
12. Merged Sam and Emma, go to others.

but did I miss the explanation (did not pickup all SAM memories) why Emma is special? Why Octagon wants her and only her? does Jim not meet aliens moral standards?