As his Defense Secretary says: "Two words, Mr President: plausible deniability."
"Area 51" is just the nickname given to a top secret air force base. In terms of the film, it can be said that he is aware of the base's existence but wasn't told that its true purpose is the housing and experimenting on alien technology.
In the movie's novelization, Whitmore did look into the file on Area 51 when he first got into office, out of curiosity, but it contained no mention of extraterrestrials. He realizes they had been falsified even for the president and wonders what other secrets his own agencies are keeping.
"Area 51" is just the nickname given to a top secret air force base. In terms of the film, it can be said that he is aware of the base's existence but wasn't told that its true purpose is the housing and experimenting on alien technology.
In the movie's novelization, Whitmore did look into the file on Area 51 when he first got into office, out of curiosity, but it contained no mention of extraterrestrials. He realizes they had been falsified even for the president and wonders what other secrets his own agencies are keeping.
If it's not broke, why fix it?
But more seriously, military technology increases to meet increasing threats. These aliens presumedly don't go looking to conquer worlds with technology anywhere close to theirs, so they don't feel the need to improve on what works well.
As an example in the real world, the USAF currently flies 3 planes that were designed and (two of them) built in the 1950's. The first flight of the B-52 was in 1952. It entered service in 1955, and the last one was built in 1962, and they are expected to continue to be used into the 2050's, almost 100 years after its first flight. The C-130 is nearly as old, and is still in production (albeit with continued improvements). And the KC-135 has been flying since the late 50's, and not planned to begin to phase out until 2023.
"Fox" is the brevity code used by NATO pilots to signal the release of an air-to-air munition; the accompanying number is used to indicate the type of munition or missile that has been fired. "Fox 3" indicates that an active radar homing missile is being fired.
While huge alien spacecraft hover over the earth's major cities, the world population watches in fear and wonder. It turns to just fear when the alien force begins to attack and their defenses prove to be impenetrable, forcing ex-fighter pilot Thomas Whitmore (Bill Pullman), now President of the United States, along with U. S. Marine Captain Steven Hiller (Will Smith), ex-scientist turned cable technician David Levinson (Jeff Goldblum), and crop duster with a drinking problem Russell Casse (Randy Quaid) to engage in a daring counterattack in hopes of saving humanity.
Independence Day is based on a screenplay written by American screenwriter Dean Devlin and German film maker Roland Emmerich (who also directed). The idea for the film is said to come from a question asking Emmerich and Devlin, who were in Europe promoting their film Stargate (1994), whether they believed in aliens. Emmerich stated that he was fascinated by the idea of an alien arrival, and further explained his response by asking the reporter to imagine what it would be like to wake up one morning and discover 15-mile-wide spaceships hovering over the world's largest cities. Emmerich then turned to Devlin and said, "I think I have an idea for our next film."
There are a number of similarities to the H.G. Wells story The War of the Worlds. Both aliens come down to Earth in what is initially thought to be meteorites. In both, the world's militaries are initially helpless against the invaders. The movie's city destroying heat beam is a larger scale versions of the novel's heat ray. Both aliens are defeated by a virus, a biological virus in the book and computer virus in the film.
There are a number of similarities to the H.G. Wells story The War of the Worlds. Both aliens come down to Earth in what is initially thought to be meteorites. In both, the world's militaries are initially helpless against the invaders. The movie's city destroying heat beam is a larger scale versions of the novel's heat ray. Both aliens are defeated by a virus, a biological virus in the book and computer virus in the film.
The beam probably hadn't reached full strength by that point. If you watch the scene of the White House's destruction, the beam does start causing damage before the big blast travels down and blows up the structure—you can clearly see fires erupting in the White House before the big blast. However, given that David had uploaded the virus to the Mother Ship, and it had infected the saucers enough to launch the attack, the saucer that Casse destroys could have been set enough in disarray that the beam wasn't up to full power. That gave Casse enough time to perform his kamikaze maneuver.
In an action film such as this, anything is possible. David is a brilliant computer and communications scientist. He was solely responsible for cracking the code used by the invaders to corrupt our satellites. If he'd figured out how that code worked, it was probably easy for him to invent a new code that would reverse or corrupt it. Although it seems that the aliens would have anticipated how we'd react and launch our counterattack, it's reasonable to say they couldn't think of everything. It's also implied that all of our current day technology is based on things we've reverse-engineered from the crashed craft. Thus, our computer technology would be based on the alien technology, which suggests that they should be compatible and that data should be able to transfer between systems easily.
The most straightforward answer is natural resources. While it would seem more logical to avoid causing mass destruction and fallout across the Earth, the aliens assume that it's better to extinguish as much life on Earth as possible, decimating cities worldwide to put the human race in disarray and unable to launch an effective counterattack. The resources the aliens yearn to plunder would primarily be fuel sources such as nuclear material. Seeing as the aliens have no regard for human life whatsoever, it would seem unfathomable to predict why they would travel light years across the universe to destroy life rather than research it. A clue to their behavior may lie in comparing how humans themselves treat their surroundings in order to survive. The aliens may have consumed everything available on their own planet, so they now wander the universe for survival rather than curiosity. There's actually a line in the film where President Whitmore explains what the aliens are doing after his telepathy attack. He says that the aliens are like locusts, moving their whole civilization to a planet until every resource is consumed and then they move on to another planet. The aliens could have been fleeing from their planet due to a dying star or some other sort of catastrophic threat to their world. Their mothership was certainly big enough to have carried a whole civilization and could have been seeking out another planet similar to their own or gathering the resources to start elsewhere. In a 1983 TV miniseries, V (1983), a race of reptilian aliens invade and occupy Earth in order to steal all of Earth's water and kidnap the human race to use as food. They arrive on Earth in ships similar to the saucers the aliens in this film use, although they aren't as large and they don't come from a mothership out in space. In many sci-fi stories, films, and TV shows, the existence of water on Earth suggests that it's a precious resource among many on Earth, so the aliens in this film could have been after our water. An exception to this would be Signs (2002) where water is actually toxic to the aliens.
He fired his Secretary of Defense, and there were no other Cabinet members accompanying him. The Vice President, Speaker of the House and all other Cabinet members were in NORAD, which the aliens destroyed. He could have appointed General Grey as acting SecDef, but he would have had to resign his military rank (only civilians can hold an office that is in line for Presidential succession). General Grey is still in uniform when they are up in the air. But in case Whitmore would have been killed, the law indeed specifies that he be succeeded by the Vice President, the Speaker of the House, or a Cabinet member. There are probably no clear regulations nor precedents in case all these persons are unavailable. The remaining authorities would probably have to declare some state of emergency or martial law, which would give local authorities (state governors etc.), the military and institutions such as the Federal Emergency Management Agency (FEMA) temporary power to form small (local) governments. In the meanwhile, a national government would have to be reassembled, elections arranged, etc. In short, the remaining authorities would have a field day determining the legitimate body in charge, so executive power is most likely shared among several persons and agencies. It's possible or even likely that there would simply be no successor President, whereby a military council assumes leadership or a special dictatorship emerges out of an unlawful coup.
The theatrical version runs more than 2 hours. Nevertheless there's also an extended version which contains more than 8 minutes of new footage. Those scenes are only plot scenes for a deeper characterization or to make the story itself more logical. Some of the scenes are quite interesting, some just redundant, but fans can purchase the extended version without seconds thoughts.
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