I've never stepped very deeply into the Sleeper/Sansha storyline, but I have a theory that I'd like to put forward in light of Random's comment and links. This may have been articulated before, but as I said, I haven't really followed things closely.
[theory]
Rogue drones, sleepers, Sansha, and the Jove
act like the elements of an adaptive immune system. As a whole, they seem to treat hostility itself as a disease or cancer to be eradicated from the body of humanity.
This immune system was relatively dormant for the first few years of the Empyrean Age, but was watching closely everything that happened in YC110 (to include what happened with the Insorum the drones were protecting for Shakor) and it just got fed up (remember how disappointed the Jove were when the Caldari and Gallente turned out to still harbor "primitive" warlike tendencies). So over several months they put together their little multidimensional door-breaching operation with isogen-5 (i.e. pixie dust/red matter) bombs planted around key gravity anchors in k-space and w-space (like Seylinn). When those blew, they switched on the full immune reaction sequence by waking up the sleepers (the long-lived memory cells of the system) and giving them a link to k-space (opening up the lymph nodes). The rogue drones play the role of helper T cells and B cells and are now working with the sleepers and Jove to propagate a new clutch of killer T cells or antibodies in the form of the resurgent Sansha menace.
In this metaphor, the "uplifted" millions are immunized cells. The trembling masses of the cluster, driven to terrific fear of increasing Sansha incursions, actually constitute the body to be saved by this system.
Capsuleers and resistant conventional forces are viruses or cancerous cells that must be eliminated.
And somewhere in w-space there's some drone/sleeper/Sansha/Jove Übermensch musing thus as he considers the state of New Eden:
I'd like to share a revelation that I've had during my time here. It came to me when I tried to classify your species and I realized that you're not actually mammals. Every mammal in this cluster instinctively develops a natural equilibrium with the surrounding environment but you do not. You move to an area and you multiply and multiply until every natural resource is consumed and the only way you can survive is to spread to another area. There is another organism in this universe that follows the same pattern. Do you know what it is? A virus. Human beings are a disease, a cancer of this cluster. You're a plague and we are the cure.
The ultimate question that this theorizing leads me to is whether the disease is conventional (and the immune system is doing a good thing) or if it is in fact an autoimmune condition and the system meant to save the body is actually tearing it apart.
[/theory]
EDIT: I posted before really thinking about whether this was fully applicable to the thread. This post could definitely derail the discussion, which is supposed to be about the chron. If mods would like to split it, that's cool.