First, I must mention that I'm a little annoyed with the way that FOX is confusing the issue with the number of episodes still left for the season. I was under the impression that it would be the full 22 episodes. FOX keeps saying that there are two episodes left until the series finale. Needless to say, most of the usual sources of information are contradictory on what that means. I hope that FOX didn't cut the number of episodes, given how much still needs to be resolved. (And I don't count the direct-to-DVD "Prison Break: Final Break" towards that amount.)
This episode continues with the growing tension between Michael and Lincoln over how to resolve the conflict with the Company. Michael is still dedicated to taking the Company down by taking control of Scylla, and Lincoln and his gang have decided that the only viable way to get Scylla is to "give the Company what they want". Considering that this is Michael's story, and has been from the beginning, there's little doubt who will end up on top.
That doesn't mean that the road has to be easy, and it doesn't mean that Michael and Lincoln are at each other's throats. The two brothers are just using different methods to achieve the same goal, so it's not about both sides shooting it out. It keeps the tension semi-logical without taking away from the dramatic benefits of having the brothers at odds.
I'm also still convinced that Christina is preparing a takeover of the Company, and that knowing this will give both Michael and Lincoln exactly what they need to take control themselves. I don't see any other solution at this point. I say that it will be both brothers, because T-Bag's betrayal looks to end Lincoln's tactic as the General's man and force him back on the run. Naturally, the survivors would (and should) end up back with Michael. This series needs to end with the surviving members of the Escape Squad working together.
I don't expect everyone to survive, but I do think that the story will come to a good end. Sara's pregnancy points to the possibility that Michael and Sara will have the kind of happy future that they should have had after the second season. I would expect a final showdown between Michael and T-Bag and the death of Self, but I'm not sure about anyone else. I would love to see a happy ending for Mahone, but I have the feeling that his number may come up before the end.
The story is no less complicated than the plot for the previous episode, but it seemed to flow a bit better and motivations were a little more straightforward. It's probably just the effect of getting back into the rhythm of the series again; the long hiatus hurt the previous episode a lot more. It also helps that the story is clearly coming to a grand finale, and thanks to the strengths of this surprising fourth season, it has the potential to meet expectations.