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At the start of Mass Effect 3 it is revealed that roughly six months have passed since the end of Mass Effect 2. During this time the Normandy SR2 has been in dry dock being refitted.

During this refit period one would assume that the Alliance would want to remove any possible Cerberus security breaches. Any incumbent computer systems, VI/AIs included, would seem to be prime suspects for any hidden Cerberus traps or back doors. Thus one of the first things I would expect Alliance Techs to do, in cleaning out any bugs, would be a complete wipe of the computer systems and installation of the latest Alliance programs and VIs.

What was the Alliance's reasoning behind not wiping the Normandy's computer systems (and consequently not deleting EDI)?

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Here's my theory, tho I have no in-universe links to back it up.

EDI essentially WAS the Normandy. The Normandy functioned as her eyes, ears, her sense of being. Chances are that her coding and functionality was deeply intertwined with all of the Normandy's systems and operations, everything from the door mechanisms to the environmental controls. While she certainly could've been extricated, I'm sure it would've taken a LOT of time and effort.

EDI could've exaggerated this too, by deliberately causing serious systems failures when she felt them nosing around the edges of her being, causing the engineers to take a slower, more cautious approach to hopefully prevent any catastrophic damage to the Normandy that would require massive repair times.

After the end of ME2, the Reapers were now HERE, and started directly attacking planets. There was no longer any denying the threat, even for the densest of council members.

So I think what happened is they were just in a rush to get as many ships pressed into service, as quickly as possible. Given that, I think they just didn't have the time to do a proper extrication of EDI from the Normandy's systems. More than likely they would've just slapped a few firewalls on her external communications systems to try to prevent communication with Cerberus.

The hastened nature of Normandy's retrofit, and her being pressed into service early would seem to be upheld by the abundant amount of crap left lying around the interior of the ship.

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    Good answer, but I think it's missing something. The problem really isn't so much with extracting EDI as it would be replacing her. Removing her is simple. (Can we say sudo rm -rf /?) However, the Alliance would then have to design a VI capable of handling all her functions. Certainly they could do this, but also keep in mind that the Normandy SR2 is a Cerberus ship - they probably couldn't just drop in any Alliance VI and expect it to work out-of-the-box. In the end, it was probably decided that it just wasn't worth the trouble. – Iszi Jan 29 '13 at 20:42
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    Alternately, maybe they just hadn't gotten around to it. The Normandy wasn't exactly planned to have launched when it did, IIRC. – Iszi Jan 29 '13 at 20:43

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