This episode is essentially broken into three movements: the end of the Starkwood showdown, Jack's reunion with Kim, and the emergence of the next crisis. Two of those movements are easy to reconcile with the overall arc of the season and the continuity of the series. The third? Only time will tell, but it may be a hard sell.
Tony's demolition job at the Starkwood facility was well-done, and in a way, set the stage for his subsequent betrayal. His interaction with the Starkwood employees didn't feel quite right from the beginning, almost as if they weren't sure what he was doing. That could be 20/20 hindsight, but the scene didn't quite ring true at the time.
Jonas was definitely off the deep end, essentially blackmailing the President into handing military authority to a defense contractor. It certainly doesn't sound very good when Jonas has bioweapons pointed at civilian targets, but it's not hard to understand why Jonas would eventually come to the conclusion that Starkwood should have that seat at the table. After all, it's just one step beyond Starkwood's current position with the government. If anything, it highlights the potential problem with handing so much power over to a mercenary enterprise.
Of course, Jonas would argue that this is just a means of restoring the power of the people over their own defense, rather than keeping that power in the hands of the federal government. But in reality, Starkwood's operatives are loyal to the organization, not the American people, or they wouldn't have been ready to kill thousands to gain more political power. That detail makes the difference: Jonas was effectively trying to stage a mini-coup.
With that all said and done, attention turns to Jack, who is fading fast. Kudos to Kiefer Sutherland, who pulled off quite the performance, selling Jack's confusion and pain realistically without going over the top. The subsequent confrontation with Agent Walker, and then his heartfelt reconciliation with Kim, were nuanced enough for his personal career highlight reel. (Despite it all, isn't it likely that Kim will defy her father and undergo the procedure? Jack has to survive somehow, after all!)
It figures that Agent Moss would die mere moments after recognizing that his attitude regarding Jack Bauer was short-sighted. That it was Tony who killed him was a bit more shocking. If this is Tony's true allegiance finally coming to light, and he was playing Jack ever since the conclusion of the General Juma threat, then the writers have a bit of explaining to do. Even with all the questions surrounding Tony's recent activities, this seems a bit out of left field.
Even so, it could be designed to bring the philosophical underpinnings of the season full circle. At this point, it's clear why the government needs someone like Jack Bauer on their side, and what can happen when someone like Jack decides that he should attend to their own interests. Now it's time to explore, through Tony, why someone like Jack would choose to retain his loyalty. With six episodes left to the season, there's plenty of time to make sense of it all.