The deaths of the three main characters are not M. Night Shyamalan’s only twists in the ending of Glass as he also introduces the secret organization known as Clover. This is seen as the sniper who kills Kevin and the guard who drowns David are both shown to have clover tattoos on their hands. This then leads to Dr. Staple revealing that she is also part of the organization whose job it is to suppress the idea of superheroes in the world.
They view superpowered beings as a threat to humanity’s development – in Staple’s words, they’re “not fair” – and so attempt to both pacify the people themselves and keep wider awareness of them in the population a secret. The group has existed for 10,000 years in some form, pretty much since the emergence of modern humanity, and today functions like any high-end secret society. They hold private meetings in restaurants to discuss plans and send Staple around the country to pacify outbreak situations.
Despite killing David and Kevin in the climax of the movie, the first objective of the Clover organization is not to simply eliminate superpowered people but rather to convince them they are ordinary. One of the central ideas of Glass that’s extended from Split is the conflation of superpowers with mental illness. In Split, it was taken as mental illness born of hardship was a way to elevate a person, but here it’s reversed, with it being suggested the very idea of superpowers is a delusion.
Staple breaks down how everything seen in the Glass franchise so far can be explained in entirely rational ways. David’s mind-reading is just an advanced magician trick. The Beast is just a man who withstood dud bullets and bent centuries-old bars. For an entire stretch in the mid-section, the movie entertains the theory that this story exists in a world where superheroes don’t exist, only for it to be smashed to pieces by the final act showdown.
Sewing the seeds of doubt was the Clover organization’s real plan. They play David, Kevin, and Elijah’s abilities as delusions of grandeur inside and out, hoping to convince the subjects and the people around them that they’re nothing more than ordinary people. Clover knows that in the real world, the barrier of belief in such impossible powers is high — it took David a whole movie to accept he was unbreakable, while originally only two of Kevin’s 23 personalities believed in The Beast – and manipulate that.
They only turn to weapons and violence when that hypothesis is rejected. At the end of Glass‘, all three superpowered characters come to embrace their powers and get support from a close loved one who fully believes the fantastical things they say. In that moment, the Clover organization failed, and they have to take drastic measures. It’s a small detail, but highly important to the films’ themes of belief.
The big twist of Glass is, in its simplest form, the same as Unbreakable‘s: Mr. Glass was behind it all. His plan was never, as repeatedly teased, to lead a terrorist attack on Philadelphia’s new tallest building. Instead, the entire showdown was a suicide mission, a literal show for the cameras, and a final step in his bid to bring superheroes to the real world.