Whitmore unintentionally sending an entire military base to their deaths by launching a desperate counterattack above the ruins of LA. Here is blaming himself for not evacuating the cities earlier, but his wife is MIA. You can just hear the desperation in his voice when he shouts at the crewman to get the Black Knights out of the battle.
President Whitmore: This isn't happening fast enough GET THEM OUT OF THERE!
Not to mention this was happening at the same time as (unseen) counterattacks in New York and Washington.
News reporter: Reports indicate that this battle has repeated itself all over the world with the exact same results.
It wasn't just the American counterattack. Every counterattack all over the world started and ended like this. The Luftwaffe engaging the destroyer over Berlin, the RAF engaging the London destroyer, the People's Liberation Army Air Force engaging the Beijing destroyer, the RSAF engaging the Singapore destroyer, the RCAF engaging the Toronto destroyer, the ROK Air Force engaging the Seoul destroyer, the list goes on. Not one was victorious.
Patricia: Is Mommy sleeping now?
Whitmore: Yeah. Mommy's sleeping.
The fact that she immediately crawls into his arms and hugs him tells you that even at all of six years old, she knows exactly what he really means. After all, if you recall his first family scene, you know they think he's a terrible liar.
The look on Hiller's face when he finds out that the air base where his fiancee and stepson were headed has been destroyed. They're alive, but he doesn't know that, and they have a similar reaction when they think he's been killed.
The novel features an extra scene just before the counterattack briefing. Hiller tries to call Jasmine and his parents. All he keeps getting is "All circuits are busy." He then starts to blame himself for not taking Jasmine with him, leading to his determination to make the aliens pay.
The scene where Russell's teenage son overhears his dad's last message... and not being able to say goodbye after all those times of thinking his dad was nothing but a loser.
While Russell's kamikaze piloting is a truly awesome moment, the scene when he makes the decision to pilot his plane directly into the alien's energy weapon is still heartbreaking:
Russell: Do me a favor. Tell my children...I love them very much...
What makes it worse is that Russell says this after looking at a picture of his children that he's taped to the inside of his plane.
A meta example - this film was the swan song for an era. It was pretty much the last big-budget special-effects movie to rely almost entirely on practical effects and models, rather than CGI.
The viral marketing website for Independence Day: Resurgence, Warof1996.com has a map of all the cities that were destroyed. Looking through it reveals how widespread and total the devastation was. Cities like Tokyo, Paris, London, Berlin, and New York were destroyed in equal measure alongside places like Pyongyang, Baghdad, Vientiane, Nairobi and Manila. All in all, 108 cities were wiped off the map in just 48 hours, with a total of 3 billion deaths.
Plus, once you consider all that mankind lost on top of the human dead. Mankind has also lost its countless treasures, artworks, monuments, and antiquities. The British Museum, the Smithsonian, and the Louvre were destroyed in the first wave, taking with them the works of humanity's greatest and often most obscure artisans as well as our historical and cultural heritage. Institutions that lasted for decades, even centuries, like Harvard, MIT, Oxford, etc are all gone. It will take many decades to rebuild, and even then it won't be the same.
Combined with Fridge Horror, in the special edition, Russell tells his ill stepson that his "mother didn't want to take her medicine, either." No further information on his wife's death is given, but it leaves open a lot of unpleasant possibilities.
The novelization goes deeper into Russell's backstory, particularly the aftermath of his abduction. Needless to say, the aliens ruined his life. After being found wandering the desert, he realized he had been implanted with false memories and tried to uncover the real ones, going to everyone from UFO abduction support groups to psychics. He became so obsessed that he didn't realize his wife was sick, and after she died, he became an alcoholic wreck. This makes his payback all the more satisfying.
While fodder for quite a bit of comedy, the scene where David is in a drunken rage and tearing a break room apart can be rough to think about. Here is a Wide-Eyed Idealist who is utterly beaten down by the universe and can do nothing in response but knock over a break room trash can, in hopes of making the world a tiny bit worse out of spite. It's only a Eureka Moment thanks to a word of concern from his father that brings him back.
The realization that not even nuclear weapons can get pass the Alien shields. Everyone is cheering thinking the Alien ship is destroyed, then the smoke clears and they see the City Destroyer is still hovering above the now destroyed Houston. Its work has been done by the humans and is ready to move on to its next target. Humanity's last line of defense its most destructive weapon...is utterly useless against the seemingly invincible invaders. In that hour Humanity died.
The final human death toll, as revealed by Resurgence's marketing? 3 billion. The human population in 1996 was around 5.8 billion, so over half the world's population was lost in the destruction of 108 cities.
Whitmore coming face-to-face with the alien. All-in-all, it's been a horrible 24 hours: the invaders have destroyed 72 cities, killed countless millions, and routed humanity's armed forces. Earth is completely at the mercy of the aliens, and he tries to find a peaceful solution, in the hopes that the creatures understand what "peace" and "coexist" are. Turns out, they don't. The aliens can't coexist with humans any more than humans can live in a house filled with cockroaches. To them, we're simply the vermin that must be exterminated.
Also, the look on Whitmore's face when he's updated about the second wave. He walks into the control room and sees a giant map of America, with black marks over Atlanta, Chicago, and Philadelphia. General Grey tells him that Europe is being hit as badly as they are, and they only have 15% of their military capability left in North America. You can definitely hear the despair in Whitmore's voice when he's told that the aliens will complete the destruction of every major city in just 36 hours.
"We're being exterminated..."
Not to mention seeing the original WTC being destroyed, knowing that a few short years later it happens in real life.
The scene in which Steve and Jasmine both believe the other is dead after finding out that El Toro was destroyed.