They disable the destroyers by uploading a computer virus into the mother ship, which is blown up with a nuke.
The Green Flame Torch
Trivia: According to the Director's commentary, Twentieth Century Fox Film Corporation did not want the film to be released under the title "Independence Day" to avoid legal complications (specifics weren't disclosed as to what the problems might be, but it's also why the abbreviation "ID4" was used). Roland Emmerich (director/writer) and Dean Devlin (writer) needed to justify the title, so they added the rousing bit right at the end of President Whitmore's speech at the hangar when he ends with, "The 4th of July will no longer be known as an American holiday...today we celebrate our Independence Day!"Super Grover
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