The fact that the Enterprise, Starfleet's most advanced ship at the time, literally fired everything head-on at the swarm and it didn't even slow it down at all as it just keeps coming closer. Realizing that this wasn't even an enemy that can be slowed down at all makes the scene terrifying.
And all of this is with Krall just trying to disable the ship, not actually destroy it. Had Krall actually wanted to destroy the Enterprise from the get-go, his swarm could probably have totally obliterated the ship in the blink of an eye.
The part with Kirk in the corridor after he shakes Krall and his men for a moment is haunting. Between the dim lights, the groaning of metal in the background, the trembling camera, the tilting corridors, and the realization that the grandest ship of the fleet is going down and there's nothing her captain or anyone can do to save her, you'd be forgiven if you were reminded of the Titanic for a second. Kirk's expression as he finally gives Sulu the order to abandon ship and looks over at Syl and her group seals it. Kirk's fear of losing lives under his command has come true yet again.
Krall. Even beyond that he's a completely psychopathic warlord, he's not a new species. Humanity produced an abomination.
The way he drains people of their life force while they struggle, scream, and are clearly in horrific pain. Legitimately one of the most disturbing things ever shown in any Star Trek media.
Jaylah describes the sheer horror of being held prisoner by him: Every so often, a captive would be taken away from the group, screams would be heard, and that person would never be seen again. Imagine being in that situation; not knowing what happens to those who are taken but aware it's not pretty, and dreading the moment when it's your turn, or that of someone close to you...
What happened to the 82 other survivors from the USS Franklin? Krall explicitly states they were all killed, but doesn't specify how.
Considering how Krall extends his lifespan by literally sucking the life out of other organic beings, it should be pretty simple to guess what happened to them. Not that it makes it any less frightening.
He does specify they were all killed in his final log entry prior to him crossing the Moral Event Horizon and utilizing the alien technology, meaning they could have died of any number of conditions.
There wasn't much time that passed between the Franklin crashing and Edison's final log. The entire crew died save for three (Edison/Krall, Le/Manas, and Wolff/Kalara), and although it's later discovered that Starfleet couldn't have done anything, the thought that your crew is dropping dead because your superiors don't care is horrifying. Krall inflicted on Jaylah and his other prisoners a similar situation to what he experienced a century before.
Syl's scalp has bony fingers that look like they belong on a facehugger from Alien, especially when they unfold.
Syl's death, where you see her literally disintegrate slowly and painfully due to the alien superweapon. Krall's cold indifference to the whole thing makes it all the more terrifying.
Perhaps worse: Given his philosophy of strength and conflict as the ultimate arbiter of value, Syl's surrender of the Arbonath piece may have been evidence to Krall that she deserved death.
The horror of the attack on Yorktown: Sulu knows what Krall is capable of, and his husband and little girl are on that station.
