Sophia was warning her people not to violate their version of the Star Trek Prime Directive - if you stay here in this place (and/or time), you will do great damage to the native population. The EBEs who have spent more than 60 years mixing with us natives want to stay.
This includes her son Thomas and his lover, played by Necar Zadegan, last seen to good effect on in the final season of 24 as President Hassan's brave wife (well, I and lots of other people have been saying how reminiscent parts of The Event are to 24). And there was more 24 stuff in the continuing saga of the weak, treacherous Republican-like Vice President tonight, too.
But the big story was the confrontation between Thomas and Sophia. Thomas, egged on by Necar (or Isabelle, the character she's playing) is set to kill his mother, and inherit her leadership of the aliens. But he can't - Sophia stares, talks, and mothers him down. And then Sophia gets Isabelle to shoot herself in the leg as a sign of feality.
So as we move on to the Fall Season Finale of The Event next week - it will return in January - we see Sophia stronger than ever, the President still behind the eight-ball, and Leila and Sean still on the run. A good mix, with anything possible ...
See also The Event Debuts on NBC ... The Event 1.2: Aliens! ... The Event 1.4: 24 Back in Action! ... The Event 1.6: Not Only Aliens, Immortals! ... The Event 1.7: The Portal and its Implications ... The Event 1.8: The "Republican" VP and the Anti-24

The Plot to Save Socrates
"a Da Vinci-esque thriller" - New York Daily News
"Sierra Waters is sexy as hell" - curled up with a good book


