While hiding out at the base under Area 51, Levison devises a plan based around giving the aliens a 'cold'. He creates a virus and uploads it to a laptop - which when delivered directly to the mothership orbiting near the Moon, will filter down to the smaller craft causing their shields to go offline for a few minutes.
The Americans ("its about time" as the helpless Brits say) send out the plan via morse-code to coordinate the attack, and its up to Goldblum and Will Smith to fly the archaic spaceship that crash landed in Roswell in 1947 straight to the mother.
They have no problem getting in, and successfully upload the virus. Unable to get away, they light cigars and deliver "the pay load" which is a huge nuke - but the first minor explosion has dislodged them, and they don't have long to get out.
Meanwhile on earth, the virus has taken longer than expected to filter down. The President leads the way in his F/A18, and after the first missiles are wasted, tries one more that makes it all the way through. "Eagle Seven. Fox 2!" Everyone else fires, as the invaders launch all their mini ships to defend the big target.
The missiles aren't doing anough damage, and the death-ray beneath the large ship starts to open - directly over the base.
Randy Quaid is the only pilot with a missile left, but it has malfunctioned. Other pilots clear the way for him, in one of the greatest action sequences ever created, and he flies directly up into the beam as it starts to generate power - after all their experiments on him, he's back!
The ship explodes and the ground crew morse-code the weakness to every other nation. It's about time.
Other ships are taken down, including ones in Egypt and elsewhere in Africa by just a few spears and shoes it seems.
Will and Jeff make it out just in time, but are eaten up in the blast radius.
They crash land to earth, almost exactly in the same Area 51 spot, and are soon picked up. They walk back as champions and kiss the girls. Up in the sky, everyone has fireworks for the 4th of July party.