So the good guys finally figure out that the visions they've been seeing of a circle with a line across it relate to the orb they blew out of space.
The crazy scientist who is out of the coma triggers it to open, and we learn that it's from a rival system to the aliens and has been fighting against them for years, and is here to help. It's all very Falling Skies.
Now it's activated, the aliens are coming to get it. Earth sends out squadrons to attack the mothership, but it's all a trap, again. Liam Helmsworth and his crew take their super-charged jets and crash land inside the mothership. They manage to capture a few ships and escape.
Around the world, meanwhile, the large ship is still drilling into the earth's core, and the President and her team are taken out by the aliens.
Jeff Goldblum has a plan to lure the mothership into the desert so they can use nuclear weapons, by using a fake signal so they go after the orb. Bill Pullman volunteers to be the pilot to take on the mothership.
As he approaches the Queen, he tries to do a Randy Quaid and an emotional sendoff but it doesn't quite work. He flies into the ship and detonates the bomb, bringing the ship down. As everyone has seen Falling Skies, they think it's a hive thing and once the Queen is dead, the others will just drop down dead too. But she isn't dead yet - she's a huge alien with reinforced armor.
Liam Helmsworth and his guys use their captured ships to light her up, and finally break the shield and get through her armor. She falls out of her exo-skeleton, and dies in a gooey mess. The other aliens all conveniently die ... except the giant drilling mothership, which starts to leave earth.
The crazy scientist tells everyone that the orb has plenty of info about weapons and inter-stellar travel, so next they can take the fight to the aliens.