This episode brings an interesting close to the Terra/Eastern Alliance storyline. However, the ending seems a touch hasty and ill-drawn, leading to some loose ends and contrived forms of deus ex machina. First, the entire idea of Apollo inhabiting another man's identity seems pointless -- he gets captured, accused of being crazy, and eventually saves the day by owning up to his identity as stranger. Why couldn't he just be himself? Everything would have followed the same. It seems a strange detour along the way.
Secondly, the Battlestar Galactica is apparently now able to use its lasers to surround a planet's atmosphere and destroy all foreign objects in the ionosphere? Really? They certainly could have used this sort of technology when fighting Cylon military planets (as in "The Living Legend").
Thirdly, the mysterious stranger recruits Apollo because he has no body, and therefore cannot be seen outside his spaceship -- and yet this doesn't stop him from talking to Apollo and to Starbuck as long as they have an "aura."
This episode is basically making up its own rules as it goes, and suggests that the writers, while unwilling to let the Eastern Alliance storyline go without a conclusion, were equally unwilling to give it a proper conclusion.