Alien Queen

The Alien Queen is is the head and matriarch of the Aliens, and commands in her pod, located inside the Harvester. She dictates complete control over her motherships, and represents the will and consciousness of her swarm.

She was retroactively mentioned as being behind the events of ID4: Independence Day (1996), and serves as the main antagonist in Independence Day: Resurgence (2016).

Rank and Position
This monstrously large alien was the commanding force behind the invading Aliens. Residing in a private and heavily guarded center pod of the Harvester, she had the ability to control nearby Aliens, and was incredibly hard to kill. She is noted for being gargantuan, extremely strong, and strategically gifted. Aside for her size, she is noted for being the only Alien known to have a mouth and vocal chords, unlike the rest of her species.

Bio-suit
The Queen may be large (roughly 100 feet tall in her bio-suit, and 30 feet tall without it), but like the rest of her species, she is vulnerable outside of her pod and her bio-mechanical suit. The Queen's bio-suit is similar to smaller ones used by the rest of her species, and it is entirely plausible that the rest of the Aliens adopted the design to emulate their Queen. It is obviously much larger than those worn by other Aliens, and emits its own protective blast shield. However, with enough bombardment (by native Alien projectile it seems), the shield generator can be disabled.

Mind control
The Queen is the central entity for all of the Aliens' ships, including her pod, with only her having an individual will outside of the hive-mind. Because of the hive-mind, any Alien would gladly die to protect the Alien Queen.

War of 1996
Though never seen, the Queen orders the Supreme Commander of a Colony mothership to attack Earth, so that the planet's core is harvested. The mission was soon a failure, and the Supreme Commander is destroyed. Nevertheless, the Queen plots revenge against mankind.

War of 2016
During the War of 2016, the Queen recieves a distress signal issued by a City destroyer that fought during the War of 1996. She then has the Harvester headed for Earth immediately, to avenge the first invasion and to rip the planet of its resources. Shortly before the arrival of the Harvester, however, the Humans target the Sphere, which they thought was another threat from outer space. The Harvester then reaches Earth and promptly disables its defense grid, before settling over the Atlantic to begin drilling towards the core of the planet.

Anticipating a counter-offensive from the humans, the Queen watches an aerial bombing human squadron approach her pod, before launching her impenetrable defenses. Shortly after, the Aliens capture president Elizabeth Lanford and take her to the Queen's pod. There, the Queen interrogated her, using Reese Tanner's body to communicate with the female president, and demanded to know where the Sphere was located. Elizabeth Lanford reveals that the Sphere has been shot down, but refused to divulge anything further, taunting the Queen that even if Lanford were to die, other people would take her place (as, unknown to her, Joshua T. Adams had). Shortly after, the Queen detected the Sphere's location and departed to track it down, but not before personally killing Lanford for pleasure.

As such, the Queen's pod detaches from the Harvester toward the signal of the Sphere's signal at Area 51. David Levinson tricks the Queen, however, by rerouting the signal to a space tug piloted by former president Thomas Whitmore, who infiltrates the Harvester and detonates cold fusion bombs directly in front of her face. The Queen, however, is shielded by her bio-mechanical suit's shield generator, and is the sole survivor of the explosion, even though her pod was destroyed and in ruins. She then engages Patricia Whitmore in battle, resulting in the loss of not only Patricia's craft, but also the Queen's shield and weaponry. The Queen then makes her way toward Area 51, with her Attackers performing a protective swarm around her. However, two humans piloting stolen Attackers, Dylan Dubrow-Hiller and Jake Morrison, attack her from behind. Together, they destroy her suit, fatally wounding her, and the Queen then makes one last roar before she falls to the ground and bleeds to her death. Because of their Queen's death, the Aliens return to the Harvester, leaving in peace without the evil Queen's hive-mind control, and the invasion ends.

Behind the Scenes

 * In the film novelization, the Queen, after being weakened, is killed by the school bus driven by David Levinson, ramming directly into her head. In the film, the Queen crumples to the ground after being fatally wounded, and bleeds to her death.
 * The Queen's death before nearly toppling over on the bus driven by David Levinson is very similar to a scene in Roland Emmerich's 1998 film Godzilla, in which the titular monster is killed by jet fighters and crushed a car.
 * The Alien Queen appears to be heavily inspired by the Xenomorph Queen from James Cameron's 1986 science-fiction action film, Aliens.
 * She appears on the Independence Day: Extinction app icon (which is based off of the film).

Other

 * It is unknown is there are other Queens and Harvesters like the Sphere said. However, this is certainly highly unlikely, because just because someone says something doesn't mean it's true (take Prince Hans from Disney's Frozen, for example). However, unlike Hans who was just a flat-out liar, the Sphere (an artificial intelligence) could have been mistaken because she saw a Harvester attacking one planet, and a Harvester attacking another. She knew that there is a Queen inside a Harvester, so she automatically thinks that there are many Harvesters and many Queens. It could definitely have been the same Queen and Harvester all along.
 * It is also unlikely that the Aliens are spread all over the universe. The movies never said so whatsoever, and their homeworld was said to be Earth-like, not universal. It is probably much more likely that the Aliens have one simple homeworld where they thrive: a planet very similar to Earth.
 * The Queen does not appear in ID4, but she was the mastermind behind the attack in that film. However, she does appear as the main antagonist in Independence Day: Resurgence. This means that she is the Big Bad of the entire franchise so far.
 * Her real name (not counting her title) is unknown.

Appearances

 * Independence Day: Resurgence (novelization)
 * Independence Day: Resurgence (film)