Twenty years after the first alien invasion in 1996, Earth is at peace. Nations have put their
differences aside and have founded the ESD, Earth Space Defense. With the pieces they salvaged from
fallen ships, they've reverse-engineered alien technology and created an alert system against
extraterrestrial threats. The ESD has set up its headquarters in Area 51 and bases on the Moon,
Mars, and Saturn's moon Rhea. What Earthlings don't know is that are aliens out there still
looking at our planet, and former president Whitmore keeps having nightmares about it. These
dreams show him the strange vision of a circular figure with a line that he can't stop drawing.
Meanwhile on the Moon base, Jake and Charlie are towing new parts of the base's defense system to
create a giant weapon. In the process, something mysteriously goes wrong and the tugs can't keep
the weapon up. Commander Jiang asks the boys to pull back, but Jake ignores orders and uses his
ship to push the weapon back up. He triggers the fusion drive, which could potentially burn down
the ship, but Jake works fast and puts the weapon back into place before that can happen. When he
returns to the base, Jiang still scolds Jake because he blames it for the mistake and grounds
him until further notice. In Area 51, General Adams is called to the base for an emergency.
The aliens that they captured twenty years ago have always been in a catatonic state until now.
They're suddenly awake and shaking in their cages. Adams wants to discuss this with the ESD Director,
but he's unreachable. It turns out David is in Africa with Floyd, a government-appointed
controller. They meet with warlord Umbutu and his rebel forces, whose headquarters are surrounded by
alien bones. They aren't happy to see David, but before things can escalate, Catherine cuts in and
assures the warriors David is with her. Apparently Catherine has been working here for a while,
studying the psychic connection that Umbutu has with the aliens. Catherine takes David to see the
only ship that landed on Earth twenty years ago. The locals had fought the aliens that came out
of this ship for ten years, and Umbutu explains that the ship lights turned on by themselves two
days ago. They also discover a giant hole in the ground, revealing the aliens had been trying to
drill into the planet's core and stopped when they blew up the mothership during the first
war. The group enters the ship and discovers the computer is sending a signal that David recognizes
as a distress call that someone already answered. Back in the Moon, Jake has a video chat with her
girlfriend Patricia, who happens to be Whitmore's daughter. Patricia informs him the International
Legacy Squadron will visit the Moon base soon, and that includes their friend Dylan, who Jake
had a fight with some years ago. Jake almost got Dylan killed during a flying test, so Patricia
wants Jake to be nice and accept it was his fault. Sometime later, the Squadron arrives and everyone
is excited to meet Dylan because he's the stepson of the first war hero Steven. During lunch,
Jake meets with Dylan and instead of being nice, he taunts him, saying Dylan was in his way again.
This makes Dylan punch him, getting the attention of Jiang. Jake covers for Dylan and says he just
fell before returning to his room, where he admits to Charlie he's taken it too far.The next day in
the medical bay in Area 51, Doctor Isaacs visits his husband Okun, the research director that fell
in a coma during the first war. To Isaacs' shock, Okun suddenly wakes up, not realizing two decades
have passed until he sees how much Isaacs has changed. Meanwhile Adams receives news that the
base on Rhea has been completely destroyed, and now they're on red alert. In Africa,
David finally gets informed of the emergency, but Catherine is still obsessed with analyzing
the circle drawings that are all over the place. Umbutu takes them to his office and shows him all
the drawings he made based on the visions he's been having since the ship woke up. The circle
looks more like some kind of contraption, and Umbutu has managed to decipher some of the aliens'
language as well. On the Moon, everyone starts panicking when they notice a whirl forming in the
atmosphere. This turns out to be a wormhole, from which a spherical machine that looks like Umbutu's
vision comes out. They send a transmission to President Lanford and David, who realizes this
sphere is a spaceship. Lanford thinks they should attack first, but David points out this isn't the
same kind of ship from the last invasion. It could come from a different alien race with different
intentions. Lanford lets the ESD council vote and attacking first wins. Jiang activates the
base's giant weapon and easily knocks the sphere down. David wants them to retrieve it to study it,
and Lanford agrees to send a team of scientists, but David must return to DC for political reasons,
which leaves David furious. Lanford makes a public announcement that they defended Earth
from a second attack. Whitmore sees it on tv and gets nervous because he can tell they aren't the
same aliens, so he thinks he should warn everyone. Patricia thinks he needs to calm down and trust
the new president. Whitmore accepts to go to bed, but when Patricia checks on him later,
she finds him gone. Meanwhile Jake understands David's frustration and wants to help. He goes
behind Jiang's back and steals a shuttle that he flies to Africa, where he picks up David, Floyd,
Umbutu, and Catherine. After a bumpy ride through the old mothership's debris field,
they find the sphere, and Jake and David get ready to retrieve it. On Earth, the US is throwing a
celebration to commemorate the anniversary of the first war victory. Whitmore interrupts Lanford's
speech to try to warn everyone, but at that moment, his head starts hurting and he collapses.
In the hospital room, Okun is drawing formulas on the walls when he suddenly suffers the same pain,
and Umbutu closely follows. People on the Moon are shocked to see a new alien mothership
arriving and coming too close to the ground. Charlie rushes to take control of the shuttle
and picks up Jake and David right before they get crushed. Adams gets the alert on Earth and
cancels the celebration while Jake takes over the piloting so Charlie can pick up the sphere
with the robot arms. It takes him a few tries to succeed, but when they're ready to go, they
discover the mothership has its own gravity and is attracting the shuttle toward it. Jiang sends
the pilots and activates the giant weapon, but the shot fails and the pilots have to come back. The
mothership returns the shots and destroys the weapon, thus Jiang orders everyone to evacuate
right before the ship flies too close and destroys a good section of the Moon, including the base.
The ESD activates the Orbital Defense System, but the mothership destroys all the satellites
before they can shoot. A few minutes later, the mothership reaches Earth, dragging down Jake's
shuttle with it. The proximity begins causing the destruction of various cities, and the ship
gravity's pulls up people and buildings alike. David realizes it wants to land on the North
Atlantic Ocean and Jake has to start pulling some crazy moves to avoid getting hit by the debris.
Lanford orders the evacuation of all coastal cities, but some boats don't get the message
in time. David's father Julius is sailing when he sees the ship arrive. He calls David to tell
him this ship is much bigger than the last one, but the call ends when the mothership lands and
Julius is hit by another boat. The elite pilots come from the Moon to help with the defenses,
but Dylan doesn't get there in time and has to watch his mother help a woman and a baby escape
before she goes down with the hospital building. Whitmore and Patricia meet with Adams in Area 51,
and Okun escapes his room to join their meeting. The aliens in the cages have gone crazy, and Okun
thinks they're celebrating. While David and the others arrive too, Whitmore sneaks into a sealed
room and releases one of the aliens to establish communication. The alien uses its tentacle to grab
Whitmore and talk through him, saying "she has arrived, she is all". Catherine shows the alien
the circle symbol, asking what it means, causing the alien to get furious. The soldiers realize the
tantrum is about to kill Whitmore, so they shoot the alien to stop it. Bullets don't do much but
Umbutu comes through and uses his blades to attack the alien. This big body is just armor, and once
it's broken the real small alien comes out, which Umbutu immediately kills. Meanwhile at the coast,
a group of siblings that just lost their parents are trying to drive away and find shelter. Among
the debris, they discover Julius' destroyed boat and the man unconscious inside. They confirm he's
still alive and take him with them. The Area 51 team scans the mothership, which helps David
understand that "she is all" means the aliens are a big hive and their huge queen just arrived. Then
a reconnaissance aircraft sends them a live feed from under the sea, showing this mothership is
drilling too. It seems they're after Earth's molten core, and if they get it they would
destroy all life as we know it. David points out that during the first war, they won by destroying
the mothership, meaning there must've been another queen inside the ship back then. That implies they
don't need to destroy this much more powerful ship, they just need to kill the queen. Lanford
authorizes a mission to find the queen, and all the pilots get ready. Drones will fly ahead to
disable the shields, then the pilots will fly cover for the bombers that will shoot cold fusion
warheads that should penetrate the hull and kill the queen. The pilots approach the mothership,
which immediately opens its defenses. The jets try their best to fly around it and maintain a
defensive posture, but the ship is too heavily guarded and it's impossible to reach the top
of the ship. After losing two bombers, Jake points out that entering the ship is the only chance they
have. Dylan agrees it's dangerous but also the only way, so Adams authorizes them to go while
ordering the others to provide backup. When the jets get inside, they're shocked to see
there's a whole ecosystem there. At that moment, Whitmore wakes up and tells Patricia the queen
knows they're coming. Patricia rushes to Adams to inform him it's a trap, but it's too late:
the queen sends a special wave that disables all the jets. The pilots begin falling to
their deaths, but they still release the bombs to try to finish the mission. Unfortunately,
the explosion doesn't hit the queen because she's surrounded by an energy field. Suddenly a second
wave comes out of the alien system and this one is so big that it disables all satellites,
the Area 51 base, and the president's bunker. Then the mothership uses the opportunity to attack the
bunker, killing everyone inside including Lanford. Moments later, the military leaders arrive at Area
51 and name Adams the new US president. Catherine shows Okun's drawings to Umbutu and he manages to
translate some of them: there are mentions of an intergalactic war and something about stopping an
enemy before it reaches Earth. This makes Umbutu realize the sphere wants to be an ally because the
aliens are also its enemy. Inside the mothership, Jake and Dylan among a few other pilots have
managed to survive the fall, so now they must hide in the ecosystem not to be caught. At the base,
Okun manages to get the capsule open with a special laser and scans the sphere, but he
can't detect any signals. Floyd comes closer to touch the sphere out of curiosity, and the smooth
surface begins absorbing his hands. After a few seconds, the sphere activates and lets go of Floyd
before it starts communicating in English, which it learned from Floyd's mind. At the same time,
the queen gets a reading on her system and decides to put on a huge piece of armor. The pilots can
only watch how the top of the mothership suddenly takes off to initiate a new attack. The sphere
begins explaining that it intercepted the aliens' distress call and came to try to warn humans,
but the humans attacked the sphere without asking questions first. The sphere's species
has fought the invading aliens before, they call the motherships "Harvester Ships" because they
go from planet to planet harvesting the cores to be used as fuel. This sphere is the only survivor
from its planet, and its system holds the key to superior technology. There's a hidden planet where
it teaches refugees from other fallen worlds how to build weapons that will defeat the invaders,
this is why the aliens are scared of it. Unfortunately now that the sphere is activated,
the queen can track it. David points out that if the queen is already coming, they could bait her
like she baited them first. Okun and David think they can hide the real sphere inside an isolation
chamber and replicate its radiation signal with a decoy inside a tug filled with cold fusion bombs,
then the queen will follow that signal into a trap. The only thing they need is some way
to track the queen, and Adams reveals he still has a radar truck from the first war. Adams and
David talk with the few pilots that are left, explaining that since the satellites are down,
someone will have to fly in manually to detonate the bombs, meaning that pilot won't survive the
mission. Patricia tries to volunteer, but Whitmore cuts in and accepts the mission, ignoring his
daughter's disapproval. Meanwhile Julius wakes up and convinces the siblings to take him to Area 51.
However they're running out of gas and moving at a glacial speed. They stop by a gas station and
find a school bus full of kids that were abandoned by the driver, so Julius takes over and with all
the kids aboard, he begins driving the bus toward Area 51. Inside the mothership, the pilots find
the aliens' hangar. Jake runs ahead to distract the aliens by insulting them and peeing on their
floor while his friends steal the jets. The aliens don't take Jake's insults well and open fire, but
before they can hit Jake, the pilots take off on the jets and pick Jake up. Immediately the aliens
begin chasing after them and closing the doors, so the pilots have to pull some extra moves to
avoid getting killed. In the heat of the battle, Jake apologizes to Dylan for almost killing him
all those years ago. After a few close calls, the pilots manage to reach the doors and escape right
before they close. Everyone at the base gets ready for the attack. Patricia watches her father leave
despite her protests and decides to fly along to help him. At that moment, Julius and the
kids arrive on the bus at the same time the queen arrives with her army. As the base and the aliens
both open fire to start a new war, David notices the bus and brings it over to his sector for
protection. The sphere is put in the isolation chamber and the queen falls for it, believing
Whitmore has the real signal. Patricia flies her jet near her dad's and says goodbye before he
faces his sacrifice. As David puts a shield around the alien army to contain the explosion, Whitmore
enters the queen's ship and detonates the bombs. For a moment, the team believes they've won, but
for some reason the alien army is still attacking and the base's huge weapon is shot down. As the
smoke clears, it's revealed the queen is still alive because she protected herself with her own
energy shield. David gets on the bus with Julius and the kids so they can drive away as the queen
begins chasing them. Every soldier on the ground returns to the base to defend the sphere from the
incoming aliens while the pilots attack the queen, whose shield keeps her safe. The boat crew notices
there are only six minutes left, and at that moment, Patricia notices that the queen puts down
her shield for a few seconds when she needs to attack. She takes advantage of this and shoots at
her weak spot, destroying the shield and leaving her vulnerable. The queen hits her jet in revenge,
and Patricia escapes with a parachute right before crashing. Then the queen tries going after her,
but at that instant Dylan and the others come back and attack the queen with her own technology.
Inside the base, the aliens find the sphere, which is guarded by Okun and Isaacs, and send a message
to her queen with the location. Dylan and his team lose control of the jets because the queen
uses her hive link to make all her technology fly around her to form a new shield. Umbutu and Floyd
rush to the isolation room to fight the aliens, but in the struggle, an alien manages to hit
Isaacs. While Umbutu and Floyd finish the aliens off, Okun has to say goodbye to his husband. With
only two minutes left, the queen arrives at the base and begins hitting the roof to try
to access the sphere. Dylan calls the jet shield a tornado and that gives Jake an idea: they activate
the manual thrusters and let the tornado form a fire whirl that expells them out of the hive. As
the queen finally breaches the base and grabs the sphere, the pilots regain control of the jets and
open fire on her, forcing her out of her armor. The queen tries to walk away and almost gets the
bus, but David drives back right before the queen falls and finally dies, releasing the sphere in
the process. Just like it happened during the first war, the death of the queen instantly stops
the drill and all the alien ships, which crash to the ground. Everyone around the world celebrates
the victory as the mothership leaves, and Okun confirms the sphere is fine. David is worried
that Earth won't survive another attack, but Okun reminds him that the sphere has a training
program on a shelter planet, so the next step for humanity is to join the intergalactic war.