The real story?
WARNING: Long post with SPOILERS. Short version: Trying to explain some of the story we don't see and the not so obvious reasons behind the plot.
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First time through the ending became very muddled for me and the twists just felt tacked on for twists sake. Random screamers popping out of nowhere and their incredible ego as well as delaying to attack and revealing later screamers types to the Alliance base till the end of the movie when they've been around for ages.
However thinking it through I came up with the following. I'd be interested to know of any flaws, other ideas or how the book shapes up. The only P Dick novel I've read is obviously Do Androids Dream of Electric Sheep, which to me doesn't share a real similarity with Bladerunner. So my version of events:
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The Screamers took over and destroyed the NEB the 6-12 months before the movie is set (tying in with the Alliance seeing no NEB activity). Whilst trawling through all the data in the NEB databanks they came across some information that the Alliance had a secret site with passage back to Earth. There is a chance that they also tried to initiate contact with Earth as a means to spread to other worlds but were found out resulting in Earth sending Jeffersons squad to nuke the place as things had gone too far (although Jefferson was fed and believed the story he iterated).
Having a legion of drones they find the site and drill through but are unable to either program the flight or fear failing at gaining launch and landing clearance with Earth. They then sabotaged the crane and planted the teddy as a just in case measure to safeguard their booty in case things went wrong.
Thus they began their scheming which we see unravel in the movie...
The Screamer AI sends out the message to the Alliance for assistance. The NEB soldier who miraculously makes his way across the desert to the Alliance base only to be torn down at the last second was in fact a Screamer, set up just to get the message there. They could have hand delivered the message but it might have led to too many complications with questioning of the soldier by the Alliance. The next screamer we meet is the Type 3. Its sole purpose is to be set up to be killed to ensure Becker, Jessica and Ross gain Joe and Jefferson's trust.
Now let me explain a bit about Becker and Ross. We know Jessica is a Type 4+, lets just consider anything this advanced a type 4, they have a self sufficient AI although still working for the good or with orders from the central screamer AI. Becker IS a type 4 also, not a type 2. He has the self sufficient AI as evidenced when interacting with the group however I believe that the knock he receives from the plutonium nuke blast messes up his programming and it reverts to a type 2 kill mechanism. It could be he simply used the old type 2 programming himself to take Jefferson out of the equation and leave Jessica free to get Joe to set up the flight but that doesn't explain him wanting to kill Joe later. Ross simply has to be a screamer, I doubt the other 2 just decided to help him out and let him shack up with them. We know they can bleed and the stunted vocabulary as well as the other 2 joking (remember self sufficient AI) that he shares the face of the type 2's could mean he is a 2. He could well have been a screamer they unintentionally bump into which Becker may have thought would be of some use but later decides it to be a mistake. I still can't think of anything really concrete for Ross's inclusion and death.
So they set off with showing J&J the NEB base having already ensured there is nothing concrete they can glean from it, maybe the chip scanner was functional to divert attention to a type 2 instead of the Commander considering more advanced versions. Meanwhile the Screamers send a main force to finally take over the Alliance base to ensure the Commander is forced down the avenue of using the shuttle. Communications by the fake 'Chuck' are intentionally dumbed down for Joe to recognise that screamers have taken over and to not put himself into a dangerous situation. The Type 3s are used as the defence force simply because they pose no real threat with their speed, just enough to scare them away from the base.
However the nuke is not something they planned for and Becker takes a severe knock causing his programming to malfunction and revert to a remnant of the older type 2 kill code still in there. Nothing of interest till they get to the hangar apart from Jessica's 'awakening'. Once access to the hangar is granted by Joe and they are inside they are confronted by Chuck. His over inflated ego and desire for revenge leads me to believe that he is indeed the reconstructed Becker but being a self sufficient AI is ignoring the master AI's original plan and just fulfilling his bloodlust. Attacking and killing Joe just after access was granted as part of the original plan would not have left room to plant the bear. Jessica 2 is either a hunter to take care of the rogue Becker/Chuck, the tracker placed to ensure the plan was carried out by Jessica 1, or possibly the intended model for the flight. End of story.
Thanks for sitting through the long post, add anything you want.