First things first: having the terrorist threat more or less ended in this episode, rather than the finale, was unexpected. It certainly threatens to steal a bit of thunder from the conclusion of the season. On the other hand, if the season finale actually focuses on Jack and the personal fallout of this day on his status (professionally, medically, and personally), then it would follow through on many of the unspoken promises made over the course of the season.
The attention given to Jack's slow but steady restoration as the master counter-terrorism agent, and the underlying argument that CTU is a necessary cog in the intelligence community machine, has been surprisingly substantial this season. For all the popular shock tactics of previous seasons (which is the only way to explain the ongoing love affair with the fifth season), there has not been a truly sustained thematic season arc in a very long time. One might even argue that it hasn't been done until now.
That attention to detail is the only reason that this latest twist makes a bit of sense. Kim was going to have to help her father somehow, and unless she was convinced to go against her father's wishes, it was going to have to be his change of heart. That meant bringing them back together against his will. The end of this episode sets that stage.
So it seems fairly clear that Jack's current activities, as well as Chloe's little tech-guru dance with Janice, will lead to the reinstallation of CTU, that Jack will be convinced that he should accept Kim's help to stay alive, and that he will learn about his grandchild. (Kim's survival, of course, is not a given in this scenario.) One might even speculate that Jack and Renee will end up rather close, given how snuggly she's been with him so far.
At the same time, Olivia's indiscretions with assassins look to come back to haunt her and her mother's administration. It appears that the predictable blackmail attempt scenario is in full effect, and it would probably work if Agent Pierce wasn't such an awesome operative. Considering the fact that Olivia never should have been Acting Chief of Staff in the first place, since Ethan's ouster was based on false pretenses, at least this rather annoying subplot should put things right before the end.
The only real complaint at this point, other than some bizarre dialogue here and there, has to be the characterization for Tony. Granted, Tony made it clear at the beginning of the season that his issues with the government and his desire to strike back over Michelle's death had never gone away. It would still be nice for Tony to explain himself more to Jack, even if just on a personal level.
After all, there's too much history between Jack and Tony to pretend that Tony's comments earlier in the day would cut it. Jack is going to want to hear a lot more on the subject. The finale looks to be giving them plenty of time in close quarters, so hopefully this will get some resolution. It just seems a bit unnecessary to have brought Tony back from a questionably handled death, only to drag the character through the mud by turning him into a domestic terrorist.