The initial plan to target the queen at the centre of the ship is revealed to be a trap - some pilots are killed, some are trapped onboard. The probe from the start turns out to be from another alien race, containing information about vastly superior knowledge and weaponry they hope humanity can use to destroy the invaders once and for all.
The aliens are determined to obtain the probe, as it could potentially lead to their downfall. A trap is set, using a transmitter to replicate the probe's radio signature, lure the queen's ship into the desert, surround it with shields, then detonate powerful bombs to kill her, using the shields to contain the blast so as to avoid collateral damage. The former President (Bill Pullman) volunteers to fly the suicide mission to deliver the bombs.
The trap technically succeeds, however the queen has not been killed, and emerges from the wreckage in a powerful bio-suit, setting after the real location of the probe, using a swarm of alien ships around her for protection. However, pilots from the earlier failed attack are in two of the ships, and manage to trigger their fusion drives to escape the alien control, then turning their weapons on the queen, finally defeating her. With the queen dead, the giant alien ship shuts off its core drill and leaves earth. The human survivors realise that with the advanced technology they've been given by the probe, they might be able to take the fight to the aliens for once.