Reginald Hargreeves always treated Vanya (Elliot Page) differently in The Umbrella Academy, and a scene in season 1 has given some insight as to why. The end of the first season of the hit Netflix show revealed that Reginald was a refugee from another planet. Before he left his home planet, he took one reminder of his old life that would haunt him for the rest of his life.
The Umbrella Academy follows the story of a group of six estranged superpowered siblings and their sister, Vanya, who doesn't initially seem to have any powers. The family is brought back together after the death of their adoptive father, Reginald. The first season explores their childhood as the crime-fighting unit called the Umbrella Academy, while Vanya was forced to watch from the sidelines. But the end of The Umbrella Academy season 1 reveals that not only does Vanya have powers, but she is also the most powerful of all the siblings.
Reginald was always aware of how powerful Vanya was, but he never wanted any of the kids to know. He had his daughter Allison, who had the power to alter reality, convince Vanya she was ordinary. Vanya's conviction that she was ordinary, coupled with her isolation from the other children, meant she had an extraordinarily lonely upbringing, overlooked and neglected by her adoptive father. But Reginald did this for a painful yet selfish reason — Vanya reminded him too much of his late wife.
When the audience first meets Vanya in The Umbrella Academy, she is introduced as a renowned violinist. While her siblings reveled in saving the world, Vanya's violin was the only thing that gave her solace. She was different than her siblings and her father resented her for that, so she couldn't turn to anyone in her family for comfort. But The Umbrella Academy season 1 finale, "The White Violin," proved that Reginald didn't resent Vanya because she was ordinary — it was because of her love for the violin. The episode revealed that Reginald was from another planet and he had to leave his dying wife behind to come to Earth. But before he left, his wife made him promise he'd take her violin with him. She wanted Reginald to give it to someone who would love it just as much as her.
He gave that violin to Vanya as a child, who took to it right away. That's why Reginald hated Vanya. It had nothing to do with her powers, but the fact that she reminded him of his late wife. The Hargreeves siblings always remembered their father as being cold and distant. But the flashback in "The White Violin" showed how sweet he was with his wife. Her death destroyed him and Vanya reminding him of her, even slightly, was too much to handle. While Reginald died before the events of The Umbrella Academy season 1, the Hargreeves' time-traveling shenanigans in the show's second season created an alternate timeline in which he was alive. That means that The Umbrella Academy season 3 will likely dive further into Reginald Hargreeves's alien origins, perhaps even giving him the opportunity to rectify his relationship with Vanya.