After some of the things said tonight, this is what I believe is going on. (The larger points anyway...The details, of course, are still unknown.)
1. Sloane is interested in bringing about some giant evil-guy scheme (having something to do with Rambaldi and Sydney.)
2. This is dangerous for Sydney (and she's the "only one who can stop him".)
3. Irina knows this, and is working to protect her daughter (using morally questionable means at times.)
4. Sloane knows that Irina is trying to thwart his plans, and is threatening her.
5. Jack knows more about it than he lets on, but even he doesn't know exactly what Sloane or Irina are up to.
That's what it looks like to me, anyway. Of course, there's always more to Alias than what we think.