This episode was all about Ben Linus and John Locke, and as such, it was practically destined to be one of the best episodes of the season. The dynamic between Locke and Ben has been evolving beautifully since the second season, and this is the logical direction for the story to take. If Ben was the unanticipated replacement for Locke, then sooner or later, the island was going to correct that situation.
While the story is relatively straightforward, matters are complicated by Ben's penchant for deception. Was Ben anticipating Locke's resurrection or not? Looking back on his reaction in the teaser, it's fairly clear that he wasn't expecting Locke to return from the dead, and he only claims to have expected it to maintain a sense of control. He can feel his power over Locke slipping away moment to moment, and he does not react well to the realization. (Note the scene in which Ben says he has no control over what is about to come out of the jungle, and it turns out to be John Locke!)
Ben's little gambit with Caesar is designed to convince Locke that he's still the one calling the shots. It's remarkably transparent, and one gets the sense that Locke is well aware of what's happening. From that point on, it's very hard to tell when Ben is being honest and what he's trying to retain what little control he still possesses. For example, why does he react so strongly to the notion that Christian is running around the island? And is he really so shocked to see those members of the Oceanic Tribe in the picture from 1977?
It's not necessary for Ben to have known about the connection between the Oceanic Tribe and the Dharma Initiative. His decision to imprison and manipulate Jack, Kate, and Sawyer already made sense within the context of the situation at the beginning of the third season. The Dharma connection would only add a new layer to the story. But if Ben remembers being taken to the Temple to be saved, as he claims, then why wouldn't he remember the Oceanic Tribe? Especially when some of them were around for at least three years?
Ben's slow but steady fatalism is so pronounced that it's hard not to believe that he will be found wanting. It's already been seen, many time over, what happens when someone fails to pass judgment. As in previous situations, there seems to be a redemptive element to the judgment. Those who are willing to change or repent are spared; those unwilling to do so are killed. In this case, it feels more like Ben has received a temporary stay of execution, based on whether or not he follows John Locke without question. It's clear that Ben, right up until the end, is considering how to take back power from Locke.
This once again seems to indicate that there is a connection of sorts between Jacob and the Cerberus smoke monster. Richard, Ben, Widmore, and Locke all talk about the will of the island, and in context, they seem to allude to Jacob. This ties into the rather old theory that there is a non-corporeal consciousness on the island that takes on apparitional and even physical form from time to time. This is exactly what Cerberus appears to do. One might wonder if they are two sides of the same coin. Was "Alex" the monster, or was it Jacob?
The nature of the Cerberus monster (an apt name, given that it seems to guard the "underworld" of the island) is more mysterious than ever. The hieroglyphics seem to show Cerberus as subservient to a representation of Anubis. The statue seen earlier in the season also seemed to be of Anubis. Anubis was the Egyptian god of the dead, charged with the protection of souls on the way to the afterlife. Anubis was also connected in some ways to rebirth, though not as strongly as Osiris. The somewhat devilish face associated with the Cerberus monster suggests that it serves in a trickster-style capacity, which would seem to fit into the theory that Cerberus sometimes takes on human form.