The Commission Could Be Working For A Post-Apocalyptic Villain
All this raises the possibility that the Commission is working for a post-apocalyptic race. When Five first jumped forward in time, he found himself in a post-apocalypse wasteland, the sole survivor of the human race. He was unable to return home, and spent years living there until he was finally approached by the Handler. Five briefly assumed the Commission would be dedicated to rewriting history and preventing the end of the world, but the Handler swiftly disabused him of that notion. She was quite relaxed about the apocalypse, and didn't even accept that it was indeed the end of everything. Instead, she referred to it as "the end of... something." It was an enigmatic comment that suggested the extinction of the human race was a necessary part of the timeline in order to allow something else to take humanity's place as the dominant species on Earth.
This may well explain the Commission's advanced technology. In the world of The Umbrella Academy, humanity never had the opportunity to develop the kind of tech used by the Commission. But perhaps this post-apocalypse race will have a closer affinity with time, and learned how to manipulate it. If that's the case - if the next dominant life-form on Earth is a race of time-sensitives - then they would have realized that human free will could alter the timeline, preventing their coming into existence in the first place. Thus they'd found the Commission, to ensure the timeline remained stable, the human race was rendered extinct, and the right conditions developed for them to come into existence. It's even possible that some of the Commission's senior management are post-humans. Certainly the Handler seemed distinctly odd, and appeared to be able to freeze time without needing any technology at all.
Related: Related: Will Ben Be Alive In Umbrella Academy Season 2?
Naturally, at this stage this is only a theory, but it fits with everything in The Umbrella Academy season 1. What's more, there would be a certain surreal irony to this idea that works perfectly with the tone and style of The Umbrella Academy. The post-apocalypse villains would essentially be using humans to police the timeline and ensure their own race was wiped out; it's the kind of crazy idea that works in this series.
What Role Could These Villains Play In The Umbrella Academy Season 2?
Assuming this theory is correct, the reality is that the end of The Umbrella Academy season 2 has seen their plans begin to fall apart. The apocalypse happened, but the Umbrella Academy students are about to try to rewrite history and avert it again. This time round, they're almost all on the same page and they're a lot more well-informed. What's more, they've already proved too much for the Commission to handle, and Five knows all the Commission's tricks. This is the post-human race's worst nightmare.
It won't be easy for them to resolve the crisis. First they'll need to locate the Umbrella Academy, which won't be easy; Five conducted a blind jump through time, meaning they could be anywhere or anywhen. Then they'll probably need to intervene directly in order to beat them; they won't be able to operate through third parties anymore. No doubt they possess a lot of tools and technology that they never passed on to the Commission; still, it remains to be seen whether or not that will be enough to beat the Umbrella Academy students. Especially if they can successfully stabilize Vanya; her power levels are off the charts, enough to pose a threat to anyone who wants to destroy them.
The interesting question, though, is whether the Commission is the only way these time-sensitives have attempted to manipulate the timeline. It's entirely possible they've taken other strategies as well, and that the Commission is simply the most extreme. If the Handler was indeed a post-human, then it's even possible they have sleeper agents planted throughout history, working hard to ensure the apocalypse happens exactly when it's supposed to. It wouldn't even be a surprise to find that these beings were somehow involved in the mysterious births of superhumans in the world of The Umbrella Academy in the first place.