Considering the fact that the producers and writers have always seen the value of the character of Alex Mahone since his creation, as evidenced by his inclusion in every season thereafter, it's about time that the Escape Squad figured out that he's valuable to them as well. After all, Mahone is just as much a victim of the Company as anyone else on the team, and Michael and Mahone working together represents a killer double threat.
The writers pulled off an interesting change of pace in this episode, because it wasn't centered on the retrieval of the next portion of Scylla (which happened very quickly and too easily in the first act). Instead, it was about Mahone and Michael's decision to save him from the Company assassin. While one can never be certain on this show, especially when it comes to strange bedfellows like the current Escape Squad, I think it's safe to say that Michael has gained Mahone's loyalty.
As usual, kudos must go to William Fichtner for bringing the necessary depth to Mahone. I also appreciated the notion that Sara helped Michael see the light and consider what would happen if he were in Mahone's place. Sara still hasn't quite found her footing yet, which is logical for the character, but serving as Michael's touchstone to his own conscience is a fair enough role.
After "Shut Down", Agent Self could have been written in a less balanced manner, but he has been given some complexities of his own. It's fun to watch him throw what little weight he has around, and this episode did a good job of delineating the boundaries of his authority and influence. I'd like to think that Michael shamed Self a bit in the process of saving Mahone, but now that the Company knows for a fact that Self is implicated with some anti-Company operation, things are going to get a lot more complicated.
While I think T-Bag's plot thread wasted a great deal of potential, it did serve the purpose of covering some background exposition on Whistler's little book. I look forward to T-Bag's next reunion with the Escape Squad, especially now that the slightly more sympathetic Gretchen is involved. Gretchen is still far from being a hero, but the writers did the expected and tried to soften her hardcore killer portrayal. Gretchen seemed like someone with nothing to lose, but that's obviously not the case.
The end of the episode could have a couple of bad implications, since the hacker (whose name never seems to stick, since he's annoying) appears to be planning his own deal for survival. Will it simply be turning on the Escape Squad, or will he try to frame Mahone? Only time will tell.