Independence Day/WMG

The destruction of New York led to the development of the Manhattan Prison in Escape from New York
Think about it. With all of the chaos that occurred, the government decides "Screw repairing Manhattan!" and throws the worst offenders in it. After Snake Plissken's little adventure, they finally start fixing things again. (Alan Moore, if you're reading this, feel free to use it in a League of Extraordinary Gentlemen segment).
 * Sorry, the Novelization of Escape from New York actually provided an explanation, and it had absolutely nothing to do with aliens.  Interesting thought, though.

The aliens are the ones from Watchmen.
made his creations too well, and they punched a hole in space time and came to an Earth without superheroes (save a few with Charles Atlas Superpowers).

Lucky for us, he was right about humanity uniting in the face of an incomprehensible evil, and the day was saved, mostly. (The fallout from the nukes—it is likely that other countries used their arsenal on daughterships—the giant UFOs raining from the sky, and the major political and economic centers of each country destroyed, means that we're going right back to Humans Are the Real Monsters a few years down the road.)

The "peace" created by this event didn't last.
See the above WMG. Humanity is going to take a long time to recover. We see looting that happened in New York and Los Angeles moments before the UFOs toasted them. A lot of people won't want to wait for civilization to come back.

Alternatively, the peace created by this event is what's necessary to create the first steps towards the United Federation Of Planets.
These events aren't mentioned in the archives because it's been a few hundred years and the stories got a little...distorted.

The peace lasted because everybody died right after the credits
The situation we leave our heroes in as the movie fades to black is even more doomtastic than the Endor Holocaust. A spacecraft "one fourth the size of the Moon" has just blown itself to smithereens; at the altitude we saw it hovering when Goldblum and Smith went to meet it, the debris is pretty much all coming down on us. Even if it was mostly hollow, there will be enough wreckage to bury the surface of Earth several kilometers deep after first incinerating it from the heat of all that junk reentering. Rocks fall, everyone dies.


 * Everyone on the surface dies. Those fortunate enough to reside in the vault-like extraterrestrial technology enhanced Area51 will survive. Their descendants emerge centuries later to form a post-apocalyptic technocracy.
 * Nope. Almost all the pieces miss the Earth, and those which do hit do only limited damage. Because THAT'S THE WAY Haruhi Suzumiya IMAGINED IT WOULD HAPPEN. (This is an AU Suzumiya, who is very into SF but doesn't assume aliens are going to be friendly...)

The city-killer saucers were hydrogen-filled dirigibles
Why did the aliens use such unreasonably gigantic spacecraft to cart around wimpy beam weapons that packed about as much punch as a pile of nuclear bombs that could fit in a modest-sized human aircraft? Why did the city killers burn so readily when shot with tiny little anti-aircraft missiles once their invulnerable energy shields were down? Why did the wrecked city killer hovering over Area 51 drift gently away to crash far off in the distance? How could they hover without Newton's third law crushing everything on the ground beneath them?

Simple—they were almost entirely filled with lighter-than-air hydrogen bladders.


 * Newton's third law: the ships were supporting themselves with some sort of technobabble graviton beam system that interacted with the earth itself, spreading out the forces through the rock underneath, rather than propelling material downwards. (Which still relies on technobabble and impossible as far as we know technology, but a lot of the physics issues people spot in the movie may work like this.)


 * Tiny little anti-aircraft missiles? That one tribe was able to take one down with spears!


 * Not necessarily, the tribe was only celebrating the defeat, there was no implication of them being the ones behind its destruction. They were just there to show how the virus and the coordinated airstrikes saved all of humanity, make the faceless benefactors visible, and overcome A Million Is A Statsistic.
 * Indeed. The Africans had to be shown as tribesmen because Reality Is Unrealistic.

The ships are huge cause the aliens never invented the transistor
The ships are full of giant vacuum tubes.

The Aliens were taken down by the virus because the tech guy had Vulcan help
Think about it. How does a human computer virus, from 1996, take down a space fairing space ship? Easily, he had help from the Vulcans from Star Trek.

The Alien Superweapons were dismantled and reverse-engineered by the army to become Hammerdown.
See Cloverfield for more details.

The film takes place during the distant past of the Tengen Toppa Gurren Lagann universe
The reason the aliens strategy involves sucking a planet dry and moving on? They're either running away from the Anti-Spirals, or working to keep the level of Spiral energy in the universe to a minimum so they don't have to worry about their own Spiral energy levels. Their technology would later be used to make the Gunmen.

President Whitman is a Republican.

 * First, Jasmine says she "voted for the other guy" and as an African-American woman (and stripper) she belongs to traditionally Democratic party-affiliated demographics. Second, Whitman is a military veteran, traditionally seen as a Republican trait.
 * On the other hand, I seem to recall, around the time the movie was released, Hal Emmerich said that the character of Whitman was inspired by Bill Clinton. Of course, that would mean that one of the only survivors of the LA attack was perhaps the only Republican African-American single mother and stripper in the US.

The Mac Virus worked because...

 * The scientists at Area 51 had been tinkering with the ship for 50 years.
 * Human computer technology is secretly based on the computers in the alien spaceship discovered in Roswell in 1947, which were reverse-engineered by human scientists.
 * The Horde of Alien Locusts were in a technological plateau, so the starfighter wasn't so obsolete as to raise immediate red flags.
 * The scientists had at least a few days to figure out how to interface their computers with the alien hardware, possibly more (note they can manually raise and lower the shields from outside the ship even before the virus is written).
 * The Horde of Alien Locusts are a hivemind, and thus all their technology is fully-integrated.
 * They have no concept of lesser races being able to breach their security, so they have no firewall technology.
 * They were downloading survey data from the advanced scout starfighter, and it was this data that the virus was uploaded into.
 * Mac paid for product placement. Macs were built with alien technology.
 * Much like Macs, the software of the invaders was designed to be incredibly simple to operate and virtually idiot-proof. The simple programming made it easy to design a virus to shut the system down.
 * The aliens programmed their computers to be compatible with human technology so they could hijack our satellite network for communications.

The alien weapon used to destroy cities is an antimatter containment and delivery system
The green beams are an antimatter containment system that delivers a small amount of antimatter onto the target. When the antimatter is in place outside the ship's shield, the containment is switched off and a huge explosion occurs. This explains - why the beam is on for some time before the explosion occurs. - how a laser-like beam can transfer enough energy to destroy a city. - why firing into the beams works at the end of the film - this shut down the containment system while the antimatter was too close to the ship and so the ship got blown up instead.
 * If ya wanna hold onto a bit of realism, it's pretty much the only way the destruction could happen in the scale it did. But maybe....just maybe...RuleOfCool is meta...Hrm...

After the end of the movie the remains of the city ships become prime thrill-seeker territory.

 * The 15 mile wide spacecraft leave ruins which judging by the movie are at least 2–4 miles tall. Tell some mountain climbers they're not going to go tackle that. Go on.

Secretary of State Nimzicky was on the alien's side, feeding them information.

 * He is nothing but disruptive to the President and withholding vital classified information, even when it wouldn't be much of a secret anymore. He is very quick to suggest nuking the city ships - maybe even hoping it will work and thus getting out of the fear of being implicated by either side.

The alien mothership runs on the Infinite Improbability Drive.

 * The improbability field generated by the drive is what generates the improbable coincidences throughout the movie, such as all the characters just happening to meet up, the cable guy just happening to decode the aliens' timing signal, their computer system just happening to be compatible with Mac OS, and, of course, their invasion just happening to take place on Independence Day weekend. Truly, their technology was their downfall.

The Aliens' ships are actually unmanned suicide weapons

 * The alien's strategy is this: make a fleet of cool starships which are incredibly big and dense. Then, make the ships' engines or cores explode as soon as it is hit with an anti-aircraft missile. Spend decades stealing cable to make the computer interface compatible with their computers and use as little memory as possible. Add a laser and invincibility to make the ship fearsome. Maybe some fighters or some cyborgs to convince the targets that these are real aliens. Then, send the ships to the target planet, let them get blown up and fall to the ground, the targets thinking they had won. 50 years later, the real ships should arrive. The nuclear winter caused by untold billions of tons of burnt ship floating in the atmosphere should have left a completely barren planet, free of trigger happy sapient creatures and |pesky biological deterrents. The aliens in the real ships clean up the debris, xenoform the planet and colonize it. This explains why a computer completely obsolete even by today's standards 'beat' the aliens, while making the extraterrestrials infinitely more powerful.
 * Punch: "Welcome to Earth." Yeah, the fighters totally were uncrewed, and if they had pilots...Also the alien who sees the laughing skull when the virus is uploaded.

In the sequel, the president will have a romance with an alien princess

 * Why? because that's the stereotype and the film is full of stereotypes. Also, he has to overcome his wife's death in some point.

The movie is actually intended as delivering a Green Aesop.

 * The mother ship contained the aliens' entire population. Thus, like so many times before, humanity is once again responsible for the total extinction of an unique form of life. Bastards!
 * Meh... They had it coming.
 * Alternatively, after making psychic contact with the apprehended alien, President Whitmore relays their method of invading a planet and stripping it clean of resources before moving on. This can be seen as a message against unchecked environmental consumption… since if you don’t regulate the use of your resources better, you will eventually use up your planet, be forced to wander space and destroy other worlds until the inhabitants of one of them finally fight back and wipe you out.

It is a vicious circle.

 * Step 1: Ca. 50 years after the arrival of the first scouts, a gigantic interstellar alien space ship comes to a planet with nice living conditions, in order to destroy or enslave all native sentient life and to colonize the planet.
 * Step 2: The natives defeat the aliens and destroy the mother ship.
 * Step 3a: No Endor Holocaust does not apply. The remnants of the huge mother ship cause devastating environmental problems. The living conditions on the planet get significantly worse.
 * Step 3b: At the same time, the native sentients experience an enormous technological leap forwards, due to all the alien stuff, free to loot and reverse-engineer for everyone.
 * Step 4: The living conditions on the planet will soon become unbearable. The natives decide to construct a gigantic interstellar space ship, one where their whole population will fit in, and to leave the planet.
 * Step 5: Even with advanced alien manufacturing technologies, the construction of the ship will last ca. 50 years. In the meantime, the natives send out smaller scout ships to seek out and explore potential candidates for planetary colonization.
 * Step 6: See Step 1.

Or they took over another star system and thus began Firefly
Jayne is obviously Major Michell's descendant!

Humans must always fight

 * While the movie seems to be making the point that it is possible for humans of all countries to unite, what it is actually saying is far more depressing: Humans always need an enemy, and the only time they will stop fighting each other is when aliens come and they can have someone else to fight with.
 * So humans are Orks?

Post war Earth is under the rule of a single world state, the Aliens living in District Nine Ghettos.

 * Overall causalties are realitivly low because the Cities where mostly evacuated. The surviving human governments band together in a loose federation to maintain order, rebuild, deal with the refugee crisis, and prepare for the next alien attack (this never comes as the Aliens where an autonomous migrant fleet which invade a planet, loot it and then take off.) Meanwhile not all the aliens died when their ships went down, so the new Earth Government is forced to do something about this new minority, and not willing to commit total genocide, build various ghettos around the world.

Postwar Earth, most of humanity is still alive
The aliens managed to destroy the first set of cities and most of their population because of the small window of time people had to escape. However, they apparently don't get to the next set of cities (which include Chicago and Houston in the Director's Cut) till the next day, giving citizens in most major cities time to escape.

In the United States in particular, New York, D.C., LA, Houston, and Chicago are confirmed to be destroyed, but as far as we know Phoenix, either San Francisco or San Diego (depending on which California city the aliens chose to target first after LA), Dallas, and Miami are all probably still intact.

Within the USA, Florida might be the best place to live if Miami, Ft. Lauderdale, Orlando, and Tampa are still intact.

It's possible also that Canada is doing relatively well. We don't know if the aliens targeted Toronto, but even if Toronto is gone, most of the rest of Canada could still be intact.


 * And it wasn't like Genre Savvy people weren't making a beeline out of their cities in the HOURS they had to do so. If Jeff Goldblum's character and his Dad were able to get out of New York and drive to Washington, millions must have gotten out of New York alone.
 * I always figured that the Dad lived outside NYC (New Jersey maybe?) and David was only able to leave NYC because he used a bike to reach his Dad.

Major Mitchell is actually Knowle Rohrer under an alias, or vice versa.
Why not? They're both played by Adam Baldwin and it would make some kind of sense given their jobs. Also, when the guy on the phone at the cable-TV-place says "I love the X-Files too", he wasn't referring to the TV show; the guy on the other end of the line was Mulder, whose viewing of some documentary on the paranormal had been interrupted so he was complaining that this would hurt his work on the X-Files. The guy on the phone was just agreeing with him to get him off the line. SO THERE, they can too take place in the same universe.

The list of targeted cities

 * The American ships:
 * In the novelization, San Francisco buys it in the first wave (four ships attacking the USA instead of the three in the movie). I would figure that the LA ship would then head to San Diego before heading towards Nevada and Arizona while the San Francisco ship heads north towards Portland, the Seattle/Tacoma urban area and into Canada (with Vancouver).
 * The DC ship razed Atlanta but somehow chose to head towards Houston while somehow ignoring Jacksonville and New Orleans.
 * The NYC ship hit Philadelphia then Chicago. Why Chicago instead of the much closer Boston and Toronto? No idea.
 * You may want to consider what tactical value those cities have and their population density. This is bordering on not showing work, but I thought inland Chicago was more densely populated than the coastal Boston at the time of filming, and you may want to consider any major military installments in the area (remember the SAC-NORAD HQ that was shot up by their fighters and the AFB where the Los Angeles F-18 group came from?). Plus, I guess the aliens were going to hit most capital cities and the most densely populated, then work their way down.
 * The European ships:
 * One ship hit Paris then is mentioned as having hit Brussels next. In the novelization, the Dutch destroy a ship in the final battle, so it might be the same one.
 * I haven't heard Independence Day UK, but I should assume one single ship hit the major British cities one after the other.
 * The rest of the world:
 * The ships sent to New Delhi, Beijing and Tokyo had a field day with a huge selection of ripe targets all around.
 * Looks like Cairo wasn't in the list of first targets despite its large population. The novelization mentions a ship in Tel Aviv. If that one ship then hit Alexandria, the timing could fit with its being destroyed while on its way to Cairo afterwards.
 * They probably decided attacking a country that might have nukes was for the best. Just because their ships have shields, doesn't mean they could protect their ground forces from being nuked off the face of the planet.
 * Sydney wasn't on the first hit list either. Maybe they hit Canberra and/or Melbourne first?
 * Or they just attacked the much larger and denser population centres in Asia first before moving to Australia and didn't have enough ships to waste on Australia in the first strike. Jakarta on it's own has half the population the entire country of Australia has. Then there's Beijing, Karachi, Delhi, Shanghai, Mumbai, Tianjin, Guangzhou, Seoul, Shenzhen, Tokyo, Dongguan, Bangkok, Wuhan, Lahore, Bangalore, Singapore, Surat, Chennai, Chongqing, Kolkata, Yangon, Shenyang, Hyderbad to destroy before you get down to cities the size of Sydney and if you are already in the process of exterminating the 1.3 billion people in China and the 1.2 billion in India, or the 270 million in Indonesia or 120 million in Japan you might want to finish the job there properly before moving down to Australia with 20 million people spread out over the entire continent.

The ship that attacked Australia was taken down by the wildlife.

 * Because the wildlife in Australia is just that dangerous.

The military is okay with the President fighting in the counterattack because it's an election year.
First, they need every pilot they can get. Second, if the President dies in the battle but humanity wins, it won't be too much of a problem that there's no President (since the last surviving successor was the Secretary of Defense, who was fired before the battle began, vacating the entire chain of succession), because that condition will only last about six months. They could even have the newly elected Congress pass a law for an emergency transition to have the new President-elect assume office immediately, rather than waiting until January 20. In the meantime, the Chairman of the Joint Chiefs will assume command of the military while the executive powers of the Federal government will devolve on the Governors of the 50 states acting in concert. In fact, due to the crisis, it's likely that special elections to refill the House of Representatives will be scheduled for within a month, at which time they will elect a new Speaker of the House, who would then resign to assume the Presidency. There is a succession plan available, and nobody is going to be starting a war in the aftermath right away, either.
 * Actually, given that Congress is unable to meet due to being dead President Whitmore can make recess appointments, meaning that he can easily designate a new Vice-President simply on his word alone. While this would only last until the next time the Senate could convene a quorum and either confirm or deny his choice, under these circumstances that time would be 'after the next election' (as a new Senate must first be elected before it can convene) so the point would be moot. In addition, General Gray is the obvious appointment for VP and confirmation for him would be a no-brainer anyway.

General Grey will be Whitmore's immediate successor as the next President; Capt. Hiller will be the President a few terms later
General Grey was the only person in the government who managed to keep a cool head besides Whitmore himself. He also provided Whitmore with trustworthy advice, in contrast to the sniveling Secretary Nimzicki. By the end of the movie, Grey and Whitmore were basically like Bash Brothers and one can easily imagine that once the 2000 election arrived in-universe, Whitmore would absolutely vouch for Grey and endorse him should he choose to run.

Just as importantly, in the aftermath of the crisis, Grey would likely have an Eisenhower-like reputation, and would almost definitely win the 2000 election.

Really the only way Grey wouldn't be elected is if he chose not to run, but in the likelihood that America would be faced with many years of rebuilding after the events of the movie, Whitmore would probably urge him to do so, knowing that he's a competent leader who'd command enough popularity and respect to hold the country together during the years of reconstruction that lay ahead.

As for the part about Will Smith's Capt. Hiller being President a few terms later, it's basically been confirmed that if Roland Emmerich and Dean Devlin get the go-ahead to make a sequel, this will be the case as long as they can get Will Smith to return.