Spartan R41: In the Halo 3 level "The Crow's Nest," we hear a Marine shout out "Shielding failed. They're down and charging," after the base is hit with an EMP. Several theories have been given for this, including actual metal plating, however Halo 3: ODST may have provided us with a link.
In the Epilogue of ODST, we see the Engineer Vergil about to give Johnson - and in effect the UNSC - vital information about the Covenant, yet his aid most likely didn't end there. As we all know, Engineers are actually Forerunner artificial lifeforms. The Bubble Shield equiptment was a UNSC crafted device, however the shield dome (which is noticeably stronger than the MJOLNIR's shield system) shares the familiar hexagonal pattern that is found on Forerunner consoles (Halo Wars) and the Sentinel shields in Halo 3. What if Vergil provided the technological know-how for the UNSC to develop it's own shields?
Now apply the Bubble Shield to a larger scale, and you've got base shielding. This is somewhat easy to do, as the base is stationary. However what's next? Possibly ship shielding, as well as personal shields for Marines and ODST.
I wouldnt be suprised at this due to the claim that the UNSC issue equipment in Halo 3 was directly related to Covenant technology. It was based off of several different Covenant technologies (of which I do not know) or so we are told.
However I do find an issue with this.
The Bubble shield, while a great tool, had a short life span. How would such a technology work over such a wide spread area with out the same draw back even running off of the bases power generators?
At best, from my point of view, they would get only a minute or two of shielding before the power drain becomes too great for the generators and it is forced to be shut down. That leaves the base vunerable.
Even worse is it looks like the current known version of the Bubble Shield has an unstable powersource as it self destructs after about 20 seconds. If it requires such a powersource it would be a huge danger to a base.
It is a very real possability that you are correct with this theory, however I just dont see it. To me the more likely explenation is a steath shielding that masks UNSC bases from Covenant detection equipment.