WARNING: The following contains spoilers for Glass, which is currently in theaters.
One of the big twists in Glass, the newest movie by M. Night Shyamalan and the concluding entry in his superhero inspired trilogy of films, is the revelation that people with supernatural abilities exist around the world. There have been sightings of people with powers for centuries, with the events of the film acting as just the latest example of people with superpowers being on the verge of exposure.
Keeping them a secret is the mission of an organization so mysterious that they don't even warrant a formal name in the narrative. There is no Phil Coulson, specific titles or giant vans with a mysterious logo stamped on the front. Instead, its members are identified by only the distinctive clover tattoo on their wrists. This organization is silent, skilled and, most importantly, efficient. This is what S.H.I.E.L.D. could look like if they were going all out in the Marvel Cinematic Universe.
For most of the film, it appears that Dr. Ellie Staple (Sarah Paulson) genuinely believes that the three supposed superpowered patients at the mental hospital -- Kevin (James McAvoy), David (Bruce Willis) and Elijah (Samuel L. Jackson) -- do not actually possess any kind of abilities. She makes compelling cases to all three men, breaking down their mental states and supposed feats, reminding them of real world explanations for their acts. There's a hint of hidden motive, but the film makes it appear as if she's on the up and up.
The eventual revelation that she knows about their powers works, but the fact that she's known all along and been targeting them makes her dangerous in an entirely new and compelling way. She has been actively working against them the entire film, shading all of her dialogue with a new level of menace. She gives no hint of the real power she possesses, and even though Elijah manages to outwit her in the end, it's only after all his other plans have been thwarted and he's been killed.
Staple's primary mission was to either convince the three that they were just suffering a mental illness or, failing that, to either break them (like when she tries to have Elijah go through brain surgery) or kill them (as with Kevin and David). There's a cold, hard efficiency to her and the soldiers under her command, which makes sense when she reveals this isn't the first time they've had to do this.
Staple reveals to her compatriots (and David in his final moments) that she'll move onto the next city with superpowered sightings and set to work containing any other people with abilities. This isn't something she's just figuring out, or bothers her morally. It's her job. The group has apparently existed long before she was born, and will continue after her -- and her failures.