There aren’t a lot of specifics currently available regarding Independence Day 2‘s story, but Emmerich has said that it will feature a second alien invasion. Because the only way for aliens to travel is through wormholes, decades have passed on Earth while only a few weeks has passed for the aliens (luckily the release of Interstellar means that modern audiences have already been briefed on the science behind this).
The upside to the time difference is that humans have had twenty years to prepare for the second invasion, and have done so by stripping down the alien technology left behind and using it to advance science and weaponry. Of course, all this could be for naught if the aliens have switched to a different OS in time for the second invasion.