The Umbrella Academy's Vanya twist was subtly revealed in the very first episode. Inspired by Gerard Way and Gabriel Bá's beloved comics, Netflix's The Umbrella Academy is the story of a dysfunctional "family" of would-be superheroes who struggle to avert the end of the world. It features Ellen Page as Vanya, the one sibling who doesn't possess any superhuman abilities at all.
In reality, the series revealed that Vanya is the most powerful of all the Umbrella Academy, able to convert sound into devastating waves of energy. Sir Reginald Hargreeves feared Vanya's uncontrollable powers, and thus repressed them and persuaded her that she was normal. The twist was hardly a surprise for anyone who had read the comics, but for people who had never encountered The Umbrella Academy before it was absolutely shocking.
Netflix's series is a smart one, though, and in fact this twist was effectively foreshadowed all the way back in the very first episode. In one flashback, Hargreeves was seen carefully monitoring every one of his adopted children as they slept. He had wires connected to the temples of their heads in order to measure brain activity, and cameras in each room to show him exactly what was going on. It was another indication of just how poor a father figure Hargreeves really was to his seven children; he viewed them as experiments, rather than people, not even bothering to step away from his work in order to wish them goodnight. But look closely at this scene, and you'll see one crucial detail; Hargreeves was monitoring Vanya as well. Like all her siblings, Vanya had wires connected to her head and a security camera monitoring showing her as she slept. Hargreeves was secretly just as interested in Vanya as he was in the others.
It's a crucial detail, and it subtly foreshadows so much of Vanya's arc. Firstly, it confirms that Vanya must have powers too; after all, why else would Sir Reginald Hargreeves subject Vanya to the same degree of monitoring as the others? It logically follows that Hargreeves has been deceiving Vanya all her life, lying to her when he tells her there is nothing "special" about her. That's all the more curious given Hargreeves has encouraged the other six to train in the use of their abilities, and it thus suggests he feared Vanya's powers.
That even fits with the harsh look he gives Vanya in one scene in another Umbrella Academy episode 1 flashback, where she suggests joining her siblings in dealing with a group of criminals. He's wondering how much she knows, or perhaps just suspects, and is even harsher than usual in the hopes of quashing her desire to be in the thick of the action. Of course, in the end The Umbrella Academy reveals that Vanya does indeed have powers; in fact, she has the potential to destroy all life on Earth. That's why Sir Reginald Hargreeves went to such lengths to suppress her powers, and why he knew an apocalypse would come should she discover her powers.
The Umbrella Academy season 1 is now streaming on Netflix.