Emmerich has completed the script for two sequels to the 1996 sci-fi - tentatively titled ID Forever Part I and ID Forever Part II - with co-writer Dean Devlin.
The Amazing Spider-Man's James Vanderbilt has now been handed the script for a rewrite, Emmerich told Entertainment Weekly.
Speaking about the overall plot of the sequels, he said: "The humans knew that one day the aliens would come back. And they know that the only way you can really travel in space is through wormholes. So for the aliens, it could take two or three weeks, but for us that's 20 or 25 years."
He continued: "It's a changed world. It's like parallel history. [Humans] have harnessed all this alien technology. We don't know how to duplicate it because it's organically-grown technology, but we know how to take an anti-gravity device and put it in a human airplane."
Emmerich added that the first part would end on a cliffhanger to set up the third instalment, and that it would mainly feature new characters.
He said: "It's still some of the same characters, but also new younger characters; it's a little bit like the sons take over."
Will Smith, Jeff Goldbum and Bill Pullman starred in the original film, which centred around an alien invasion that took place on America's annual Independence Day holiday.
The film grossed over $816 million (£520 million) at the box office worldwide.
Bill Pullman recently confirmed that he will be involved in the project, while Will Smith has yet to sign up.
Watch a trailer for Independence Day below: