Corrected entry: In the scene where David shows everyone how he can penetrate the fortress, he specifically says the only way to disable the shields in all the ships is to detonate a bomb in the mothership (he says it quickly towards the end of his little speech so pay attention) - But the shields go down way before they detonate the bomb, the shields go down as soon as they upload the virus.
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Correction: David clearly says during his demonstration and I quote: "If we plant a virus into that mother ship it's gonna filter down into all the corresponding ships below." Then a few sentences later he says: "We then upload the virus, set off some kind of explosion which'll disable it."(It being the mother ship, not the shield.) So the primary purpose of the bomb was to destroy the mother ship (it couldn't be attacked by fighters since it wasn't in our atmosphere). The shields on the other ships would already be down when this happened.
Andreas[DK]