The Umbrella Academy: What Does The Ending Really Mean?

6. The Commission Will Return

Five may have killed the Handler, but it'd be folly to think that's the end of the Commission's involvement in the storyline. It's a big organisation, and there'll be someone who can step up to take her place.

The Umbrella Academy are actively working to prevent the apocalypse, and are now meddling even further in established history. That's the exact sort of thing the Commission aims to prevent. They need things to go as planned, including the apocalypse.

They can't simply allow the Umbrella Academy to get away with stealing a briefcase and running amok through time. They'll need to take a different approach, but their goal is to always ensure things happen as they're supposed to, so they can't suddenly just disappear.