3. It Takes Place In An Alternate History Where Humans Have Utilized Alien Tech
Note the word "utilized." According to director Emmerich, "It's a changed world. It's like parallel history. Humans have harnessed all of this alien technology. We don't know how to duplicate it because it's organically-grown technology, but we know how to take an antigravity device and put it in a human airplane." That opens up a world of possibilities for how humanity might defend the planet upon the alien's return. And according to Emmerich, the humans of Independence Day were very aware that one day, the alien invaders would in fact come back. Building from that, one would suspect that they've been busy preparing, and are ready to use the creature's own weaponry against them.