So, 9 was a visually entrancing movie that had an excellent, if not altogether new premise. The world is at war, everything is being destroyed by giant robot monsters, and a scientist uses a combination of alchemy and simple mechanics to create a bunch of little walking sockpuppet people to carry on after he is gone.
Pretty early on in the film, one of the little sockpuppet dudes accidentally powers up a giant evil machine using a gear with alchemical symbols on it-- which happens to be the thing that the scientist uses to create the sockpuppet things (something we know but the sockpuppets don't, at this point). The giant evil machine ends up killing another one of the sockpuppers: it sucks its life-essence out of it a la the Skeksis.
It turns out that the human race was destroyed when a technological achievement known as "The Machine," which is...a sentient machine that can build other sentient machines, turns against humanity and sends its armies of machines to kill them. The Machine is the thing that sucks the life essence out of the sock puppet.
Now, here is where my version of events differed from the movie's version.
I totally thought that the Machines took over the world because they were powered by the sentient life essence of living creatures. So to build more of themselves, they kept sucking the souls out of human beings until all the humans were gone, and then they died out, too, because they had run out of lives to use to create their own. I thought the sock puppets were created by the scientist by stealing life essences back from the machines, and that the sock puppets' mission was going to be to steal more sentient life essences back from the machines to recreate humanity: that "souls" were transient and only needed a vessel for them. So the humans were all stuck inside these machines with nowhere to go, and they could be removed from the machines and put into new "bodies."
I also noticed that the first one of the sockpuppets to die was the mechanical whiz of the group, and that the Machine started building new machines when it sucked out that sockpuppet's soul. But then the second one to die was the big, dumb, loyal bruiser of the group, and when the Machine sucked out that one, it switched from being clever to being more force-oriented. So I thought that this was confirmation of what I thought the plot was: it is still the same soul, just in a different body.
Instead, it turned out that the sockpuppets were basically little horcruxes: the scientist split his soul into nine pieces in a desperate attempt to preserve himself, not humanity. And then the sockpuppets who got sucked up by the Machine in the meantime are completely lost and they just have to free their souls, which look like badly rendered versions of the ghosts from Casper.
They made a huge deal about how they couldn't destroy the machine because the souls (or pieces of souls) were stuck inside, which seemed a bit odd when all that happened after they freed them is they got to go to heaven Presumably if this is all that was happening, they could've gotten them out after shutting the machine down, or they would have gone to heaven when the machine died.
So, yeah, I was disappointed that the big mystery in the script was not that intellectually or ethically challenging, at least compared to what I was expecting it to be!