The film is a modern retelling of the story of Atlantis.
Credit for this should go to SF Debris.
The tale of Atlantis is nearly as old as western civilization itself. It was said to be a great continent ruled by a powerful people. But, they were corrupt and decadent, and sought to impose their will upon the world. They invaded Europe, defeating all the primitive nations that resisted. Then, they attacked Greece, and Athens was able to rally the city-states into fighting back. The moral Greeks were able to defeat the Atlantians, and soon after, the island of Atlantis was destroyed.
The parallels in Independence Day are very clear. The aliens live in a mothership that's the size of a small moon, and may actually have been a moon at some point. For countless millennia, they have been roaming the galaxy, wiping out native civilizations and stealing their resources. Due to their vastly advanced technology, no one has been able to stop them.
Until they attack Earth. The humans are initially just as helpless as the many civilizations the aliens had defeated. But, we have an ace up our sleeve: the ship that crashed in Roswell. Human ingenuity has allowed us to find a working understanding of their technology, enough to create a backdoor into their computer systems. Humans can also think creatively, while the aliens have never encountered the possibility that someone might be able to gain access. Their lack of creativity is what ultimately dooms them and allows the humans to win.
