What does Jake download?

[Kyrenka]

So I was watching the special edition D3 and checked out the deleted scene when one came up where Jake downloads "something" for Trudy but what is he downloading?

[Taronyu Leleioae]

I wouldn't say it's a deleted scene.  There are 3 versions of the film plus the later version of the script (which was deviated from a little).

Film in theatres
Film re-released with more scenes in theatres
Full extended version on DVD with even more scenes, plus the deleted/alternate and never finished scenes (such as the dreamhunt).


What he is downloading, are the pictures and technical information on the ayVitrayä Utral (Tree of Souls) & ayVitrayä Ramunong (Well of Souls aka the location) which is the Na'vi people's most sacred and important place for its most direct connection to Eywa.  (Although even Jake doesn't understand how important nor capable ayVitrayä Utral is until after the failure to transfer Grace's spirit and memories permanently to her Avatar.)

This is to smuggle back to give Colonel Quaritch "intel" on how to threaten/attack/defeat the Omatikaya people.  Where Judy and particularly Jake feel horrible about doing, but they are caught in the middle.  Trudy is the carrier (mail delivery) since she makes trips back and forth to Hell's Gate.  In the script, there is some minor additional information in that Grace knows that Jake has been playing a balance.

[Blue Elf]

What he is downloading, are the pictures and technical information on the ayVitrayä Utral (Tree of Souls) & ayVitrayä Ramunong (Well of Souls aka the location) which is the Na'vi people's most sacred and important place for its most direct connection to Eywa.  (Although even Jake doesn't understand how important nor capable ayVitrayä Utral is until after the failure to transfer Grace's spirit and memories permanently to her Avatar.)

As said in talk between Quaritch and Jake earlier in the movie:
You'll speak like scientist, but report to me (not exact, but I'm lazy to find that scene)

So it's report for Quaritch, no matter what exact data he writes there.

[Taronyu Leleioae]

From the published working script.  
http://www.imsdb.com/scripts/Avatar.html

Obviously the finished film scene is slightly different.  
But this gives you the answer to your question...

TIME CUT -- Grace is scanning through images and Jake stops
         her on one -- a 3D aerial shot of the strange arched
         formation.
         
                                JAKE
                   That's it.
         
                             GRACE
                   Vitraya Ramunong -- The Well of Souls.
                   It's their most sacred place.
         
         She moves the virtual camera, and we seem to fly around the
         Well of Souls, catching only a glimpse of the interior.
         
                                                                     76.
         
         
         
                             GRACE
                   Something big is going on in there,
                   biologically. I'd die to get samples, but
                   outsiders are strictly forbidden.
         
         TIME CUT -- Jake looks through the pressure window at HUMAN
         GRACE and NORM outside. Wearing masks, they are taking
         readings from some time-series experiments Grace has set up.
         
         As TRUDY watches, JAKE works fast to download Grace's images
         of the Well of Souls onto a memory chip.
         
                             TRUDY
                   They're coming back.
         
         Jake pulls the chip, then hesitates. Torn by what he is
         doing.
         
                             TRUDY
                   If you don't give him something, he's
                   gonna shut us down.
         
         He hands her the chip and she slips it into a pocket of her
         flight-suit just as Grace and Norm enter from the airlock.
         
                                JAKE
                   Hey, guys.
                                                                   CUT TO:

[archaic]

JAKE
"Am I still with Augustine?"

QUARITCH
"On paper. You walk like one of her
science pukes, you quack like one, but
you report to me. Can you do that for
me son?

JAKE
"Hell yeah, sir."

QUARITCH
"Well alright then."

[Kyrenka]

ah thanks for the reply, makes sense now. I sound quite dumb but... what really would of happened if the Tree of Souls was destroyed?

[Rotobull cz]

I don't want to think, what would happened. It must have been catastrophic. 
I think, that some of extended scenes should be in movie. For example scene where Grace explains, what happened in the school or undone scene, where was P. Selfridge out of Hellgate buildings and where Grace told him, that they need more time, because Omaticaya live in the Hometree very long.

[archaic]

Every Na'vi on Pandora, along with most of the rest of the animal kingdom would turn up at Hell's Gate, over run it's defenses and slaughter every single last human inside, before reducing the whole compound to rubble and ashes.

Possibly.

[Rotobull cz]

Every Na'vi on Pandora, along with most of the rest of the animal kingdom would turn up at Hell's Gate, over run it's defenses and slaughter every single last human inside, before reducing the whole compound to rubble and ashes.

And then Humans would started to bomb every place on Pandora, where could Na'vi live.
So Pandora would has been destroyed.  
Slaughter. Interesting, you put out one letter and you have got wholly different word (in meaning od word).  

[archaic]

Dang it, here I am back at my fanfic again.

There is a delicate political tight rope to walk when the next ISV turns up at Pandora.
Jake can't them away in case they nuke them from orbit, or fire large chunks of rock at them from orbit.
The RDA needs to be careful, if they go to far they risk seriously brutal reprisals on Hell's Gate occupants.
But if the Na'vi do that, then we're back to the rain of destruction from space.