After changing the game in a big way in the previous episode, the writers were going to have to pull things together and establish a new status quo sooner or later. This episode tossed out a few red herrings right from the start, and didn't stop until the final frame. For an episode that could have been a letdown, this was a promising way to transition into the next phase of the season.
It seemed like the end of the previous episode would leave Michael and the Escape Squad on the run from both the Company and Homeland Security, and the beginning of the episode certainly began on that road. Between that and Self's sudden ruthlessness, it felt like the shift would be an easy adjustment. I certainly wasn't expecting Homeland Security to figure out Self's true colors so quickly.
Between the possibility of a new arrangement with Homeland Security and their subsequent betrayal of the Escape Squad, what seemed to be simple became an ugly mess. To be honest, I'm not sure what kind of position Michael and the others found themselves in at the end of the episode. The Company is still looking for them, and they're still looking to get back at Self and retrieve Scylla for their own devices, but it's unclear whether or not they're active fugitives from the law. (I would assume they are, but their legal status has been murky for a while.)
The bottom line appears to be this: Michael and the others must fend off the Company long enough to get Scylla back from Self and get it into the right hands. There's no telling how long that will remain the status quo; it's entirely possible that another twist could come along and send the story in a completely different direction. That's what makes this episode such a success. It handles the chaos borne of Self's betrayal so well that everything still feels within the writers' control.
Hanging over everything is Michael's health situation, which is probably the only plot element that demands to be resolved sooner rather than later. The last thing I want to see is a mid-season cliffhanger where Michael collapses, apparently on death's door. It's far too predictable, and even if the pacing of the season means that Michael has only been suffering his attacks for a few days, it's beginning to get tedious.
It is, however, just a small part of the story, and the rest of it is working just fine. The good is far outweighing the bad. If this is the last season, then I must admit, against all expectations, that this has been one great last hurrah.